cfa97200252eecb2b8dfe20d9d65cd5afd0f3ba3 max Thu May 28 02:37:57 2020 -0700 more OMIM hgc changes, refs #18419 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 460a48e..32ee090 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -1,26851 +1,26843 @@ /* hgc - Human Genome Click processor - gets called when user clicks * on something in human tracks display. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include <float.h> #include "obscure.h" #include "hCommon.h" #include "hash.h" #include "binRange.h" #include "bits.h" #include "memgfx.h" #include "hvGfx.h" #include "portable.h" #include "regexHelper.h" #include "errAbort.h" #include "dystring.h" #include "nib.h" #include "cheapcgi.h" #include "htmshell.h" #include "cart.h" #include "jksql.h" #include "dnautil.h" #include "dnaseq.h" #include "fa.h" #include "fuzzyFind.h" #include "seqOut.h" #include "hdb.h" #include "spDb.h" #include "hui.h" #include "hgRelate.h" #include "htmlPage.h" #include "psl.h" #include "cogs.h" #include "cogsxra.h" #include "bed.h" #include "cgh.h" #include "agpFrag.h" #include "agpGap.h" #include "ctgPos.h" #include "contigAcc.h" #include "ctgPos2.h" #include "clonePos.h" #include "bactigPos.h" #include "rmskOut.h" #include "xenalign.h" #include "isochores.h" #include "simpleRepeat.h" #include "cpgIsland.h" #include "cpgIslandExt.h" #include "genePred.h" #include "genePredReader.h" #include "pepPred.h" #include "peptideAtlasPeptide.h" #include "wabAli.h" #include "genomicDups.h" #include "est3.h" #include "rnaGene.h" #include "tRNAs.h" #include "gbRNAs.h" #include "encode/encodeRna.h" #include "hgMaf.h" #include "maf.h" #include "stsMarker.h" #include "stsMap.h" #include "rhMapZfishInfo.h" #include "recombRate.h" #include "recombRateRat.h" #include "recombRateMouse.h" #include "stsInfo.h" #include "stsInfo2.h" #include "mouseSyn.h" #include "mouseSynWhd.h" #include "ensPhusionBlast.h" #include "cytoBand.h" #include "knownMore.h" #include "snp125.h" #include "snp125Ui.h" #include "snp132Ext.h" #include "snp.h" #include "snpMap.h" #include "snpExceptions.h" #include "snp125Exceptions.h" #include "snp125CodingCoordless.h" #include "cnpIafrate.h" #include "cnpIafrate2.h" #include "cnpLocke.h" #include "cnpSebat.h" #include "cnpSebat2.h" #include "cnpSharp.h" #include "cnpSharp2.h" #include "delHinds2.h" #include "delConrad2.h" #include "dgv.h" #include "dgvPlus.h" #include "tokenizer.h" #include "softberryHom.h" #include "borkPseudoHom.h" #include "sanger22extra.h" #include "ncbiRefLink.h" #include "ncbiRefSeqLink.h" #include "refLink.h" #include "hgConfig.h" #include "estPair.h" #include "softPromoter.h" #include "customTrack.h" #include "trackHub.h" #include "hubConnect.h" #include "sage.h" #include "sageExp.h" #include "pslWScore.h" #include "lfs.h" #include "mcnBreakpoints.h" #include "fishClones.h" #include "featureBits.h" #include "web.h" #include "dbDb.h" #include "jaxOrtholog.h" #include "dnaProbe.h" #include "ancientRref.h" #include "jointalign.h" #include "gcPercent.h" #include "genMapDb.h" #include "altGraphX.h" #include "geneGraph.h" #include "stsMapMouse.h" #include "stsInfoMouse.h" #include "dbSnpRs.h" #include "genomicSuperDups.h" #include "celeraDupPositive.h" #include "celeraCoverage.h" #include "sample.h" #include "axt.h" #include "axtInfo.h" #include "jaxQTL.h" #include "jaxQTL3.h" #include "wgRna.h" #include "ncRna.h" #include "gbProtAnn.h" #include "hgSeq.h" #include "chain.h" #include "chainDb.h" #include "chainNetDbLoad.h" #include "chainToPsl.h" #include "chainToAxt.h" #include "netAlign.h" #include "stsMapRat.h" #include "stsInfoRat.h" #include "stsMapMouseNew.h" #include "stsInfoMouseNew.h" #include "vegaInfo.h" #include "vegaInfoZfish.h" #include "ensInfo.h" #include "scoredRef.h" #include "blastTab.h" #include "hdb.h" #include "hgc.h" #include "genbank.h" #include "pseudoGeneLink.h" #include "axtLib.h" #include "ensFace.h" #include "bdgpGeneInfo.h" #include "flyBaseSwissProt.h" #include "flyBase2004Xref.h" #include "affy10KDetails.h" #include "affy120KDetails.h" #include "encode/encodeRegionInfo.h" #include "encode/encodeErge.h" #include "encode/encodeErgeHssCellLines.h" #include "encode/encodeStanfordPromoters.h" #include "encode/encodeStanfordPromotersAverage.h" #include "encode/encodeIndels.h" #include "encode/encodeHapMapAlleleFreq.h" #include "hapmapSnps.h" #include "hapmapAllelesOrtho.h" #include "hapmapAllelesSummary.h" #include "sgdDescription.h" #include "sgdClone.h" #include "tfbsCons.h" #include "tfbsConsMap.h" #include "tfbsConsSites.h" #include "tfbsConsFactors.h" #include "simpleNucDiff.h" #include "bgiGeneInfo.h" #include "bgiSnp.h" #include "bgiGeneSnp.h" #include "botDelay.h" #include "vntr.h" #include "zdobnovSynt.h" #include "HInv.h" #include "bed5FloatScore.h" #include "bed6FloatScore.h" #include "pscreen.h" #include "jalview.h" #include "flyreg.h" #include "putaInfo.h" #include "gencodeIntron.h" #include "cutter.h" #include "switchDbTss.h" #include "chicken13kInfo.h" #include "gapCalc.h" #include "chainConnect.h" #include "dv.h" #include "dvBed.h" #include "dvXref2.h" #include "omimTitle.h" #include "dless.h" #include "gv.h" #include "gvUi.h" #include "protVar.h" #include "oreganno.h" #include "oregannoUi.h" #include "pgSnp.h" #include "pgPhenoAssoc.h" #include "pgSiftPred.h" #include "pgPolyphenPred.h" #include "bedDetail.h" #include "ec.h" #include "transMapClick.h" #include "retroClick.h" #include "mgcClick.h" #include "ccdsClick.h" #include "gencodeClick.h" #include "memalloc.h" #include "trashDir.h" #include "kg1ToKg2.h" #include "wikiTrack.h" #include "grp.h" #include "omicia.h" #include "atomDb.h" #include "pcrResult.h" #include "twoBit.h" #include "itemConf.h" #include "chromInfo.h" #include "gbWarn.h" #include "lsSnpPdbChimera.h" #include "mammalPsg.h" #include "net.h" #include "jsHelper.h" #include "virusClick.h" #include "gwasCatalog.h" #include "parClick.h" #include "mdb.h" #include "yaleGencodeAssoc.h" #include "itemDetailsHtml.h" #include "trackVersion.h" #include "numtsClick.h" #include "geneReviewsClick.h" #include "bigBed.h" #include "bigPsl.h" #include "bedTabix.h" #include "longRange.h" #include "hmmstats.h" #include "aveStats.h" #include "trix.h" #include "bPlusTree.h" #include "customFactory.h" #include "iupac.h" static char *rootDir = "hgcData"; #define LINESIZE 70 /* size of lines in comp seq feature */ struct cart *cart; /* User's settings. */ char *seqName; /* Name of sequence we're working on. */ int winStart, winEnd; /* Bounds of sequence. */ char *database; /* Name of mySQL database. */ char *organism; /* Colloquial name of organism. */ char *genome; /* common name, e.g. Mouse, Human */ char *scientificName; /* Scientific name of organism. */ struct hash *trackHash; /* A hash of all tracks - trackDb valued */ void printLines(FILE *f, char *s, int lineSize); char mousedb[] = "mm3"; #define NUMTRACKS 9 int prevColor[NUMTRACKS]; /* used to optimize color change html commands */ int currentColor[NUMTRACKS]; /* used to optimize color change html commands */ int maxShade = 9; /* Highest shade in a color gradient. */ Color shadesOfGray[10+1]; /* 10 shades of gray from white to black */ Color shadesOfRed[16]; boolean exprBedColorsMade = FALSE; /* Have the shades of red been made? */ int maxRGBShade = 16; struct bed *sageExpList = NULL; char ncbiOmimUrl[255] = {"https://www.ncbi.nlm.nih.gov/omim/"}; struct palInfo { char *chrom; int left; int right; char *rnaName; }; /* See this NCBI web doc for more info about entrezFormat: * https://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html */ char *entrezFormat = "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=%s&term=%s&doptcmdl=%s&tool=genome.ucsc.edu"; char *entrezPureSearchFormat = "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=%s&details_term=%s[%s] "; char *ncbiGeneFormat = "https://www.ncbi.nlm.nih.gov/gene/%s"; char *entrezUidFormat = "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=%s&list_uids=%d&dopt=%s&tool=genome.ucsc.edu"; /* db=unists is not mentioned in NCBI's doc... so stick with this usage: */ char *unistsnameScript = "https://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=unists"; char *unistsScript = "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="; char *gdbScript = "http://www.gdb.org/gdb-bin/genera/accno?accessionNum="; char *cloneDbScript = "https://www.ncbi.nlm.nih.gov/clone?term="; char *traceScript = "https://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&val="; char *genMapDbScript = "http://genomics.med.upenn.edu/perl/genmapdb/byclonesearch.pl?clone="; char *uniprotFormat = "http://www.uniprot.org/uniprot/%s"; char *dbSnpFormat = "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s"; char *clinVarFormat = "https://www.ncbi.nlm.nih.gov/clinvar/?term=%s[clv_acc]"; /* variables for gv tables */ char *gvPrevCat = NULL; char *gvPrevType = NULL; /* initialized by getCtList() if necessary: */ struct customTrack *theCtList = NULL; /* getDNA stuff actually works when the database doesn't exist! */ boolean dbIsFound = FALSE; /* forwards */ char *getPredMRnaProtSeq(struct genePred *gp); void doAltGraphXDetails(struct trackDb *tdb, char *item); char* getEntrezNucleotideUrl(char *accession) /* get URL for Entrez browser on a nucleotide. free resulting string */ { char url[512]; safef(url, sizeof(url), entrezFormat, "Nucleotide", accession, "GenBank"); return cloneString(url); } void printNcbiGeneUrl(FILE *f, char *gene) /* Print URL for Entrez browser on a nucleotide. */ { fprintf(f, ncbiGeneFormat, gene); } void printEntrezNucleotideUrl(FILE *f, char *accession) /* Print URL for Entrez browser on a nucleotide. */ { fprintf(f, entrezFormat, "Nucleotide", accession, "GenBank"); } void printEntrezEstUrl(FILE *f, char *accession) /* Print URL for Entrez browser on a nucleotide. */ { fprintf(f, entrezFormat, "nucest", accession, "GenBank"); } void printEntrezProteinUrl(FILE *f, char *accession) /* Print URL for Entrez browser on a protein. */ { fprintf(f, entrezFormat, "Protein", accession, "GenPept"); } static void printEntrezPubMedUrl(FILE *f, char *term) /* Print URL for Entrez browser on a PubMed search. */ { fprintf(f, entrezFormat, "PubMed", term, "DocSum"); } static void printEntrezPubMedPureSearchUrl(FILE *f, char *term, char *keyword) /* Print URL for Entrez browser on a PubMed search. */ { fprintf(f, entrezPureSearchFormat, "PubMed", term, keyword); } void printEntrezPubMedUidAbstractUrl(FILE *f, int pmid) /* Print URL for Entrez browser on a PubMed search. */ { fprintf(f, entrezUidFormat, "PubMed", pmid, "Abstract"); } void printEntrezPubMedUidUrl(FILE *f, int pmid) /* Print URL for Entrez browser on a PubMed search. */ { fprintf(f, entrezUidFormat, "PubMed", pmid, "Summary"); } void printEntrezGeneUrl(FILE *f, int geneid) /* Print URL for Entrez browser on a gene details page. */ { fprintf(f, entrezUidFormat, "gene", geneid, "Graphics"); } static void printEntrezOMIMUrl(FILE *f, int id) /* Print URL for Entrez browser on an OMIM search. */ { char buf[64]; snprintf(buf, sizeof(buf), "%d", id); fprintf(f, entrezFormat, "OMIM", buf, "Detailed"); } void printSwissProtAccUrl(FILE *f, char *accession) /* Print URL for Swiss-Prot protein accession. */ { fprintf(f, uniprotFormat, accession); } static void printSwissProtProteinUrl(FILE *f, char *accession) /* Print URL for Swiss-Prot NiceProt on a protein. */ { char *spAcc; /* make sure accession number is used (not display ID) when linking to Swiss-Prot */ spAcc = uniProtFindPrimAcc(accession); if (spAcc != NULL) { printSwissProtAccUrl(f, accession); } else { fprintf(f, uniprotFormat, accession); } } static void printSwissProtVariationUrl(FILE *f, char *accession) /* Print URL for Swiss-Prot variation data on a protein. */ { if (accession != NULL) { fprintf(f, "\"http://www.expasy.org/cgi-bin/get-sprot-variant.pl?%s\"", accession); } } static void printOmimUrl(FILE *f, char *term) /* Print URL for OMIM data on a protein. */ { if (term != NULL) { fprintf(f, "\"https://www.ncbi.nlm.nih.gov/omim/%s\"", term); } } static void printEntrezUniSTSUrl(FILE *f, char *name) /* Print URL for Entrez browser on a STS name. */ { fprintf(f, "\"%s&term=%s\"", unistsnameScript, name); } static void printUnistsUrl(FILE *f, int id) /* Print URL for UniSTS record for an id. */ { fprintf(f, "\"%s%d\"", unistsScript, id); } /* Print URL for GDB browser for an id * GDB currently inoperative, so have temporarily disabled this function * static void printGdbUrl(FILE *f, char *id) { fprintf(f, "%s", id); } */ static void printCloneDbUrl(FILE *f, char *clone) /* Print URL for Clone Registry at NCBI for a clone */ { fprintf(f, "\"%s%s\"", cloneDbScript, clone); } static void printTraceTiUrl(FILE *f, char *name) /* Print URL for Trace Archive at NCBI for a trace id (TI) */ { fprintf(f, "\"%s%s\"", traceScript, name); } static void printTraceUrl(FILE *f, char *idType, char *name) /* Print URL for Trace Archive at NCBI for an identifier specified by type */ { fprintf(f, "\"%s%s%%3D%%27%s%%27\"", traceScript, idType, name); } static void printGenMapDbUrl(FILE *f, char *clone) /* Print URL for GenMapDb at UPenn for a clone */ { fprintf(f, "\"%s%s\"", genMapDbScript, clone); } static void printFlyBaseUrl(FILE *f, char *fbId) /* Print URL for FlyBase browser. */ { fprintf(f, "\"http://flybase.net/.bin/fbidq.html?%s\"", fbId); } static void printBDGPUrl(FILE *f, char *bdgpName) /* Print URL for Berkeley Drosophila Genome Project browser. */ { fprintf(f, "\"http://www.fruitfly.org/cgi-bin/annot/gene?%s\"", bdgpName); } char *hgTracksPathAndSettings() /* Return path with hgTracks CGI path and session state variable. */ { static struct dyString *dy = NULL; if (dy == NULL) { dy = newDyString(128); dyStringPrintf(dy, "%s?%s", hgTracksName(), cartSidUrlString(cart)); } return dy->string; } char *hgcPathAndSettings() /* Return path with this CGI script and session state variable. */ { static struct dyString *dy = NULL; if (dy == NULL) { dy = newDyString(128); dyStringPrintf(dy, "%s?%s", hgcName(), cartSidUrlString(cart)); } return dy->string; } void hgcAnchorSomewhere(char *group, char *item, char *other, char *chrom) /* Generate an anchor that calls click processing program with item * and other parameters. */ { char *tbl = cgiUsualString("table", cgiString("g")); char *itemSafe = cgiEncode(item); printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%s&table=%s\">", hgcPathAndSettings(), group, itemSafe, chrom, winStart, winEnd, other, tbl); freeMem(itemSafe); } void hgcAnchorPosition(char *group, char *item) /* Generate an anchor that calls click processing program with item * and group parameters. */ { char *tbl = cgiUsualString("table", cgiString("g")); printf("<A HREF=\"%s&g=%s&i=%s&table=%s\">", hgcPathAndSettings(), group, item, tbl); } void hgcAnchorWindow(char *group, char *item, int thisWinStart, int thisWinEnd, char *other, char *chrom) /* Generate an anchor that calls click processing program with item * and other parameters, INCLUDING the ability to specify left and * right window positions different from the current window*/ { printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%s\">", hgcPathAndSettings(), group, item, chrom, thisWinStart, thisWinEnd, other); } void hgcAnchorJalview(char *item, char *fa) /* Generate an anchor to jalview. */ { struct dyString *dy = cgiUrlString(); printf("<A HREF=\"%s?%s&jalview=YES\">", hgcName(), dy->string); dyStringFree(&dy); } void hgcAnchorTranslatedChain(int item, char *other, char *chrom, int cdsStart, int cdsEnd) /* Generate an anchor that calls click processing program with item * and other parameters. */ { char *tbl = cgiUsualString("table", cgiString("g")); printf("<A HREF=\"%s&g=%s&i=%d&c=%s&l=%d&r=%d&o=%s&table=%s&qs=%d&qe=%d\">", hgcPathAndSettings(), "htcChainTransAli", item, chrom, winStart, winEnd, other, tbl, cdsStart, cdsEnd); } void hgcAnchorPseudoGene(char *item, char *other, char *chrom, char *tag, int start, int end, char *qChrom, int qStart, int qEnd, int chainId, char *db2) /* Generate an anchor to htcPseudoGene. */ { char *encodedItem = cgiEncode(item); printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%s&db2=%s&ci=%d&qc=%s&qs=%d&qe=%d&xyzzy=xyzzy#%s\">", hgcPathAndSettings(), "htcPseudoGene", encodedItem, chrom, start, end, other, db2, chainId, qChrom, qStart, qEnd, tag); } void hgcAnchorSomewhereDb(char *group, char *item, char *other, char *chrom, char *db) /* Generate an anchor that calls click processing program with item * and other parameters. */ { printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%s&db=%s\">", hgcPathAndSettings(), group, item, chrom, winStart, winEnd, other, db); } void hgcAnchor(char *group, char *item, char *other) /* Generate an anchor that calls click processing program with item * and other parameters. */ { hgcAnchorSomewhere(group, item, other, seqName); } void writeFramesetType() /* Write document type that shows a frame set, rather than regular HTML. */ { fputs("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Frameset//EN\">\n", stdout); } void htmlFramesetStart(char *title) /* Write DOCTYPE HTML and HEAD sections for framesets. */ { /* Print start of HTML. */ writeFramesetType(); puts("<HTML>"); char *meta = getCspMetaHeader(); printf("<HEAD>\n%s<TITLE>%s</TITLE>\n</HEAD>\n\n", meta, title); freeMem(meta); } boolean clipToChrom(int *pStart, int *pEnd) /* Clip start/end coordinates to fit in chromosome. */ { static int chromSize = -1; if (chromSize < 0) chromSize = hChromSize(database, seqName); if (*pStart < 0) *pStart = 0; if (*pEnd > chromSize) *pEnd = chromSize; return *pStart < *pEnd; } struct genbankCds getCds(struct sqlConnection *conn, char *acc) /* obtain and parse the CDS, errAbort if not found or invalid */ { char query[256]; sqlSafef(query, sizeof(query), "select c.name from %s,%s c where (acc=\"%s\") and (c.id=cds)", gbCdnaInfoTable,cdsTable, acc); char *cdsStr = sqlQuickString(conn, query); if (cdsStr == NULL) errAbort("no CDS found for %s", acc); struct genbankCds cds; if (!genbankCdsParse(cdsStr, &cds)) errAbort("can't parse CDS for %s: %s", acc, cdsStr); return cds; } void printCappedSequence(int start, int end, int extra) /* Print DNA from start to end including extra at either end. * Capitalize bits from start to end. */ { struct dnaSeq *seq; int s, e, i; struct cfm *cfm; if (!clipToChrom(&start, &end)) return; s = start - extra; e = end + extra; clipToChrom(&s, &e); printf("<P>Here is the sequence around this feature: bases %d to %d of %s. " "The bases that contain the feature itself are in upper case.</P>\n", s, e, seqName); seq = hDnaFromSeq(database, seqName, s, e, dnaLower); toUpperN(seq->dna + (start-s), end - start); printf("<PRE><TT>"); cfm = cfmNew(10, 50, TRUE, FALSE, stdout, s); for (i=0; i<seq->size; ++i) { cfmOut(cfm, seq->dna[i], 0); } cfmFree(&cfm); printf("</TT></PRE>"); } void printBand(char *chrom, int start, int end, boolean tableFormat) /* Print all matching chromosome bands. */ /* Ignore end if it is zero. */ { char sband[32], eband[32]; boolean gotS = FALSE; boolean gotE = FALSE; if (start < 0) return; gotS = hChromBand(database, chrom, start, sband); /* if the start lookup fails, don't bother with the end lookup */ if (!gotS) return; /* if no end chrom, print start band and exit */ if (end == 0) { if (tableFormat) printf("<TR><TH ALIGN=left>Band:</TH><TD>%s</TD></TR>\n",sband); else printf("<B>Band:</B> %s<BR>\n", sband); return; } gotE = hChromBand(database, chrom, end-1, eband); /* if eband equals sband, just use sband */ if (gotE && sameString(sband,eband)) gotE = FALSE; if (!gotE) { if (tableFormat) printf("<TR><TH ALIGN=left>Band:</TH><TD>%s</TD></TR>\n",sband); else printf("<B>Band:</B> %s<BR>\n", sband); return; } if (tableFormat) printf("<TR><TH ALIGN=left>Bands:</TH><TD>%s - %s</TD></TR>\n",sband, eband); else printf("<B>Bands:</B> %s - %s<BR>\n", sband, eband); } void printPosOnChrom(char *chrom, int start, int end, char *strand, boolean featDna, char *item) /* Print position lines referenced to chromosome. Strand argument may be NULL */ { printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, chrom, start+1, end); printf("%s:%d-%d</A><BR>\n", chrom, start+1, end); /* printBand(chrom, (start + end)/2, 0, FALSE); */ printBand(chrom, start, end, FALSE); printf("<B>Genomic Size:</B> %d<BR>\n", end - start); if (strand != NULL && differentString(strand,".") && isNotEmpty(strand)) printf("<B>Strand:</B> %s<BR>\n", strand); else strand = "?"; if (featDna && end > start) { char *tbl = cgiUsualString("table", cgiString("g")); strand = cgiEncode(strand); printf("<A HREF=\"%s&o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&strand=%s&table=%s\">" "View DNA for this feature</A> (%s/%s)<BR>\n", hgcPathAndSettings(), start, (item != NULL ? cgiEncode(item) : ""), chrom, start, end, strand, tbl, trackHubSkipHubName(database), trackHubSkipHubName(hGenome(database))); } } void printPosOnScaffold(char *chrom, int start, int end, char *strand) /* Print position lines referenced to scaffold. 'strand' argument may be null. */ { char *scaffoldName; int scaffoldStart, scaffoldEnd; if (!hScaffoldPos(database, chrom, start, end, &scaffoldName, &scaffoldStart, &scaffoldEnd)) { printPosOnChrom(chrom, start,end,strand, FALSE, NULL); return; } printf("<B>Scaffold:</B> %s<BR>\n", scaffoldName); printf("<B>Begin in Scaffold:</B> %d<BR>\n", scaffoldStart+1); printf("<B>End in Scaffold:</B> %d<BR>\n", scaffoldEnd); printf("<B>Genomic Size:</B> %d<BR>\n", scaffoldEnd - scaffoldStart); if (strand != NULL) printf("<B>Strand:</B> %s<BR>\n", strand); else strand = "?"; } void printPos(char *chrom, int start, int end, char *strand, boolean featDna, char *item) /* Print position lines. 'strand' argument may be null. */ { if (sameWord(organism, "Fugu")) /* Fugu is the only chrUn-based scaffold assembly, so it * has non-general code here. Later scaffold assemblies * treat scaffolds as chroms.*/ printPosOnScaffold(chrom, start, end, strand); else printPosOnChrom(chrom, start, end, strand, featDna, item); } void samplePrintPos(struct sample *smp, int smpSize) /* Print first three fields of a sample 9 type structure in * standard format. */ { if ( smpSize != 9 ) errAbort("Invalid sample entry!\n It has %d fields instead of 9\n", smpSize); printf("<B>Item:</B> %s<BR>\n", smp->name); printf("<B>Score:</B> %d<BR>\n", smp->score); printf("<B>Strand:</B> %s<BR>\n", smp->strand); printPos(smp->chrom, smp->chromStart, smp->chromEnd, NULL, TRUE, smp->name); } void bedPrintPos(struct bed *bed, int bedSize, struct trackDb *tdb) /* Print first bedSize fields of a bed type structure in * standard format. */ { char *strand = NULL; if (bedSize >= 4 && bed->name[0] != 0) { char *label = "Item", *tdbLabel = NULL; if (tdb && ((tdbLabel = trackDbSetting(tdb, "bedNameLabel")) != NULL)) label = tdbLabel; printf("<B>%s:</B> %s<BR>\n", label, bed->name); } if (bedSize >= 5) { if (!tdb || !trackDbSetting(tdb, "noScoreFilter")) { char *scoreLabel = trackDbSettingOrDefault(tdb, "scoreLabel", "Score"); printf("<B>%s:</B> %d<BR>\n", scoreLabel, bed->score); } } if (bedSize >= 6) { strand = bed->strand; } printPos(bed->chrom, bed->chromStart, bed->chromEnd, strand, TRUE, bed->name); } void genericHeader(struct trackDb *tdb, char *item) /* Put up generic track info. */ { if (item != NULL && item[0] != 0) cartWebStart(cart, database, "%s (%s)", tdb->longLabel, item); else cartWebStart(cart, database, "%s", tdb->longLabel); } void printItemDetailsHtml(struct trackDb *tdb, char *itemName) /* if track has an itemDetailsHtml, retrieve and print the HTML */ { char *tableName = trackDbSetting(tdb, "itemDetailsHtmlTable"); if (tableName != NULL) { struct sqlConnection *conn = hAllocConn(database); struct itemDetailsHtml *html, *htmls; // if the details table has chrom/start/end columns, then use these to lookup html if (sqlColumnExists(conn, tableName, "chrom")) { char *chrom = cgiString("c"); int start = cgiInt("o"); int end = cgiInt("t"); htmls = sqlQueryObjs(conn, (sqlLoadFunc)itemDetailsHtmlLoad, sqlQueryMulti, "select name, html from %s where \ name = '%s' and \ chrom = '%s' and \ start = '%d' and \ end = '%d'", tableName, itemName, chrom, start, end); } // otherwise, assume that the itemName is unique else htmls = sqlQueryObjs(conn, (sqlLoadFunc)itemDetailsHtmlLoad, sqlQueryMulti, "select name, html from %s where name = '%s'", tableName, itemName); for (html = htmls; html != NULL; html = html->next) printf("<br>\n%s\n", html->html); itemDetailsHtmlFreeList(&htmls); hFreeConn(&conn); } } char *getIdInUrl(struct trackDb *tdb, char *itemName) /* If we have an idInUrlSql tag, look up itemName in that, else just * return itemName. */ { char *sql = trackDbSetting(tdb, "idInUrlSql"); char *id = itemName; if (sql != NULL) { char query[1024]; sqlSafef(query, sizeof(query), sql, itemName); struct sqlConnection *conn = hAllocConn(database); id = sqlQuickString(conn, query); hFreeConn(&conn); } return id; } char *getUrlSetting(struct trackDb *tdb, char* urlSetting) /* get the "url" setting for the current track */ { char *url; if (sameWord(urlSetting, "url")) url = tdb->url; else url = trackDbSetting(tdb, urlSetting); return url; } void printIframe(struct trackDb *tdb, char *itemName) /* print an iframe with the URL specified in trackDb (iframeUrl), can have * the standard codes in it (like $$ for itemName, etc) */ { char *url = getUrlSetting(tdb, "iframeUrl"); if (url==NULL) return; char *eUrl = replaceInUrl(url, itemName, cart, database, seqName, winStart, winEnd, tdb->track, FALSE, NULL); if (eUrl==NULL) return; char *iframeOptions = trackDbSettingOrDefault(tdb, "iframeOptions", "width='100%%' height='1024'"); // Resizing requires the hgcDetails pages to include a bit of javascript. // // Explanation how this works and why the javascript is needed: // http://stackoverflow.com/questions/153152/resizing-an-iframe-based-on-content // In short: // - iframes have a fixed size in html, resizing can only be done in javascript // - the iframed page cannot call the resize() function in the hgc html directly, as they have // been loaded from different webservers // - one way around it is that the iframed page includes a helper page on our server and // send their size to the helper page (pages can call functions of included pages) // - the helper page then sends the size back to hgc (pages on the same server can // call each others' functions) // width='%s' height='%s' src='%s' seamless scrolling='%s' frameborder='%s' printf(" \ <script> \ function resizeIframe(height) \ { \ document.getElementById('hgcIframe').height = parseInt(height)+10; \ } \ </script> \ \ <iframe id='hgcIframe' src='%s' %s></iframe> \ <p>", eUrl, iframeOptions); } void printCustomUrlWithLabel(struct trackDb *tdb, char *itemName, char *itemLabel, char *urlSetting, boolean encode, struct slPair *fields) /* Print custom URL specified in trackDb settings. */ { char urlLabelSetting[32]; // replace the $$ and other wildchards with the url given in tdb char *url = getUrlSetting(tdb, urlSetting); //char* eUrl = constructUrl(tdb, url, itemName, encode); if (url==NULL || isEmpty(url)) return; char *eUrl = replaceInUrl(url, itemName, cart, database, seqName, winStart, winEnd, tdb->track, encode, fields); if (eUrl==NULL) return; /* create the url label setting for trackDb from the url setting prefix */ safef(urlLabelSetting, sizeof(urlLabelSetting), "%sLabel", urlSetting); char *linkLabel = trackDbSettingOrDefault(tdb, urlLabelSetting, "Outside Link:"); // if we got no item name from hgTracks or the item name does not appear in the URL // there is no need to show the item name at all if (isEmpty(itemName) || !stringIn("$$", url)) { printf("<A TARGET=_blank HREF='%s'>%s</A><BR>",eUrl, linkLabel); return; } printf("<B>%s </B>",linkLabel); printf("<A HREF=\"%s\" target=_blank>", eUrl); if (sameWord(tdb->table, "npredGene")) { printf("%s (%s)</A><BR>\n", itemName, "NCBI MapView"); } else { char *label = itemName; if (isNotEmpty(itemLabel) && differentString(itemName, itemLabel)) label = itemLabel; printf("%s</A><BR>\n", label); } //freeMem(&eUrl); small memory leak } void printCustomUrlWithFields(struct trackDb *tdb, char *itemName, char *itemLabel, boolean encode, struct slPair *fields) /* Wrapper to call printCustomUrlWithLabel with additional fields to substitute */ { char urlSetting[10]; safef(urlSetting, sizeof(urlSetting), "url"); printCustomUrlWithLabel(tdb, itemName, itemLabel, urlSetting, encode, fields); } void printCustomUrl(struct trackDb *tdb, char *itemName, boolean encode) /* Wrapper to call printCustomUrlWithLabel using the url setting in trackDb */ { printCustomUrlWithFields(tdb, itemName, itemName, encode, NULL); } void printOtherCustomUrlWithFields(struct trackDb *tdb, char *itemName, char *urlSetting, boolean encode, struct slPair *fields) /* Wrapper to call printCustomUrlWithLabel to use another url setting other than url in trackDb e.g. url2, this allows the use of multiple urls for a track to be set in trackDb. */ { printCustomUrlWithLabel(tdb, itemName, itemName, urlSetting, encode, fields); } void printOtherCustomUrl(struct trackDb *tdb, char *itemName, char* urlSetting, boolean encode) /* Wrapper to call printCustomUrlWithLabel to use another url setting other than url in trackDb e.g. url2, this allows the use of multiple urls for a track to be set in trackDb. */ { printCustomUrlWithLabel(tdb, itemName, itemName, urlSetting, encode, NULL); } void genericSampleClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int smpSize) /* Handle click in generic sample (wiggle) track. */ { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct sample *smp; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("genericSampleClick track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); /*errAbort( "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start);*/ sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); smp = sampleLoad(row+hasBin); samplePrintPos(smp, smpSize); } } void showBedTopScorers(struct bed *bedList, char *item, int start, int max) /* Show a list of track items sorted by descending score, * with current item highlighted. * max is upper bound on how many items will be displayed. */ { int i; struct bed *bed; puts("<B>Top-scoring elements in window:</B><BR>"); for (i=0, bed=bedList; bed != NULL && i < max; bed=bed->next, i++) { if (sameWord(item, bed->name) && bed->chromStart == start) printf(" <B>%s</B> ", bed->name); else printf(" %s ", bed->name); printf("(%s:%d-%d) %d<BR>\n", bed->chrom, bed->chromStart+1, bed->chromEnd, bed->score); } if (bed != NULL) printf("(list truncated -- more than %d elements)<BR>\n", max); } void showBedTopScorersInWindow(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int maxScorers, char *filterTable, int filterCt) /* Show a list of track items in the current browser window, ordered by * score. Track must be BED 5 or greater. maxScorers is upper bound on * how many items will be displayed. If filterTable is not NULL and exists, * it contains the 100K top-scorers in the entire track, and filterCt * is the threshold for how many are candidates for display. */ { struct sqlResult *sr = NULL; char **row = NULL; struct bed *bedList = NULL, *bed = NULL; char table[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; char query[512]; if (filterTable) { /* Track display only shows top-scoring N elements -- restrict * the list to these. Get them from the filter table */ hasBin = hOffsetPastBin(database, hDefaultChrom(database), filterTable); sqlSafef(query, sizeof(query), "select * from %s order by score desc limit %d", filterTable, filterCt); } else { if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("showBedTopScorersInWindow track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromEnd > %d and " "chromStart < %d order by score desc", table, seqName, winStart, winEnd); } sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+hasBin, 5); if (!filterTable || ( sameString(bed->chrom, seqName) && bed->chromStart < winEnd && bed->chromEnd > winStart)) { slAddHead(&bedList, bed); } else bedFree(&bed); } sqlFreeResult(&sr); if (bedList == NULL) return; slReverse(&bedList); showBedTopScorers(bedList, item, start, maxScorers); } void getBedTopScorers(struct sqlConnection *conn, struct trackDb *tdb, char *table, char *item, int start, int bedSize) /* This function determines if showTopScorers is set in trackDb and also */ /* if the filterTopScorers setting is on. Then it passes the relevant */ /* settings to showBedTopScorersInWindow() so that the top N scoring */ /* items in the window are listed on the details page */ { char *showTopScorers = trackDbSetting(tdb, "showTopScorers"); char *filterTopScorers = trackDbSetting(tdb,"filterTopScorers"); boolean doFilterTopScorers = FALSE; char *words[3]; char cartVar[512]; int filterTopScoreCt = 0; char *filterTopScoreTable = NULL; safef(cartVar, sizeof cartVar, "%s.%s", table, "filterTopScorersOn"); if (filterTopScorers != NULL) { if (chopLine(cloneString(filterTopScorers), words) == 3) { doFilterTopScorers = sameString(words[0], "on"); filterTopScoreCt = atoi(words[1]); filterTopScoreTable = words[2]; } } if (bedSize >= 5 && showTopScorers != NULL) { /* list top-scoring elements in window */ int maxScorers = sqlUnsigned(showTopScorers); doFilterTopScorers = cartCgiUsualBoolean(cart, cartVar, doFilterTopScorers); if (doFilterTopScorers && hTableExists(database, filterTopScoreTable)) { /* limit to those in the top N, from table */ safef(cartVar, sizeof cartVar, "%s.%s", table, "filterTopScorersCt"); filterTopScoreCt = cartCgiUsualInt(cart, cartVar, filterTopScoreCt); } else /* show all */ filterTopScoreTable = NULL; showBedTopScorersInWindow(conn, tdb, item, start, maxScorers, filterTopScoreTable, filterTopScoreCt); } } void linkToOtherBrowser(char *otherDb, char *chrom, int start, int end); void linkToOtherBrowserExtra(char *otherDb, char *chrom, int start, int end, char *extra); static void printCompareGenomeLinks(struct trackDb *tdb,char *name) /* if "compareGenomeLinks" exists then a table of the same name in n different databases is sought. if a row exist in the other db table matching the current item, then a link is printed */ { char *setting = trackDbSettingClosestToHome(tdb,"compareGenomeLinks"); if (setting == NULL) return; struct sqlConnection *conn = hAllocConn(database); // Need only to connect to one db if (conn == NULL) return; char *words[20]; setting = cloneString(setting); int ix,cnt = chopLine(setting, words); char query[512]; char extra[128]; boolean gotOne = FALSE; for (ix=0;ix<cnt;ix++) { char *db = words[ix]; // db.table.column=title or db.table=title or db=title char *table,*column = "name"; char *title = strchr(words[ix],'='); if (title==NULL) // Must have title continue; *title = '\0'; title++; if ((table = strchr(words[ix],'.')) == NULL) table = tdb->table; else { *table++ = '\0'; // assigns before advance if ((words[ix] = strchr(table,'.')) != NULL) { *words[ix] = '\0'; column = ++words[ix]; // advance before assigns } } sqlSafef(query,sizeof(query),"select chrom,chromStart,chromEnd from %s.%s where %s=\"%s\";", db,table,column,name); struct sqlResult *sr = sqlGetResult(conn, query); if (sr == NULL) continue; char **row = sqlNextRow(sr); if (row == NULL) continue; char *chrom = *row++; int beg = atoi(*row++); int end = atoi(*row); if (!gotOne) { gotOne = TRUE; printf("<P>The item \"%s\" has been located in other genomes:\n<UL>\n",name); } printf("<LI>"); safef(extra,sizeof(extra),"%s=full",tdb->track); linkToOtherBrowserExtra(db, chrom, beg, end, extra); printf("%s</A></LI>\n",strSwapChar(title,'_',' ')); sqlFreeResult(&sr); } hFreeConn(&conn); freeMem(setting); if (gotOne) printf("</UL>\n"); else printf("<P>Currently the item \"%s\" has not been located in another genome.\n",name); } void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize, boolean onlyDiff, int blockNo); void doAtom( struct trackDb *tdb, char *item) { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; //struct bed *bed; char query[512]; struct sqlResult *sr; char **row; //boolean firstTime = TRUE; int start = cartInt(cart, "o"); //struct sqlConnection *conn = hAllocConn(database); char *user = cfgOption("db.user"); char *password = cfgOption("db.password"); struct sqlConnection *sc; struct atom ret; genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("mafPrettyOut track %s not found", tdb->table); #if 0 sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, escapedName, seqName, start); sr = sqlGetResult(conn, query); printf("<B>This is the item you clicked on:</B><BR>\n"); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 4); bedPrintPos(bed, 4, tdb); } sqlFreeResult(&sr); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", table, escapedName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+hasBin, 4); if (bed->chromStart != start) { htmlHorizontalLine(); firstTime = FALSE; printf("<B>Another instances on %s:</B><BR>\n",database); bedPrintPos(bed, 4, tdb); } } sqlFreeResult(&sr); #endif sc = sqlConnectRemote("localhost", user, password, "hgFixed"); sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, item); sr = sqlGetResult(sc, query); printf("<B>Atom %s instances ('*' marks item you clicked on)</B><BR>\n",item); printf("<PRE>\n"); //printf("Ins#\tSpecies\t\tChrom\tStart\tEnd\tStrand\n"); printf( " # %-10s %-5s %12s %12s %10s %s %-10s %-10s\n", "species","chrom", "start", "end", "length", "strand","fivePrime","threePrime"); while ((row = sqlNextRow(sr)) != NULL) { atomStaticLoad(row, &ret); //atomOutput(&ret, stdout, '\t', '\n'); linkToOtherBrowser(ret.species, ret.chrom, ret.start, ret.end); if (sameString(ret.chrom, seqName) && (start == ret.start) && sameString(ret.species, database)) printf("* "); else printf(" "); printf( "%4d %-10s %-5s %12d %12d %10d %c %-10s %-10s\n", ret.instance, ret.species,ret.chrom, ret.start + 1, ret.end, ret.end - ret.start + 1, ret.strand[0],ret.fivePrime,ret.threePrime); } printf("</A>"); sqlFreeResult(&sr); if (!sameString("atom20080226d", table)) return; printf("<TABLE>"); printf("<THEAD>"); printf("<TBODY>"); printf("<TR><TH>"); printf("Suh Trees<BR>\n"); printf("<IMG src=http://hgwdev.gi.ucsc.edu/~braney/suhTrees/%s.tt.png><BR>",item); printf("<TD><IMG src=http://hgwdev.gi.ucsc.edu/~braney/suhTrees/%s.gt.png><BR>",item); printf("<TR><TH>"); printf("NJ Trees<BR>\n"); printf("<IMG src=http://hgwdev.gi.ucsc.edu/~braney/njTrees/%s.tt.png><BR>",item); printf("<TD><IMG src=http://hgwdev.gi.ucsc.edu/~braney/njTrees/%s.gt.png><BR>",item); printf("<TR><TH>"); /* printf("Gap UPGMA Trees<BR>\n"); printf("<IMG src=http://hgwdev.gi.ucsc.edu/~braney/gap992Trees/%s.tt.png><BR>",item); printf("<TD><IMG src=http://hgwdev.gi.ucsc.edu/~braney/gap992Trees/%s.gt.png><BR>",item); printf("</TABLE>"); */ return; char buffer[4096]; struct mafFile *mf; safef(buffer, sizeof buffer, "/gbdb/hgFixed/%s/%s.maf",table, item); mf = mafMayOpen(buffer); if (mf != NULL) { mafFileFree(&mf); mf = mafReadAll(buffer); struct mafAli *mafAli; int count = 1; int numBlocks = 0; for (mafAli=mf->alignments; mafAli; mafAli = mafAli->next) numBlocks++; for (mafAli=mf->alignments; mafAli; mafAli = mafAli->next) { printf("<BR><B>Multiple Alignment Block %d of %d</B><BR>", count, numBlocks); mafPrettyOut(stdout, mafAli, 70, FALSE, count++); if (mafAli->next != NULL) { struct mafAli *next = mafAli->next; struct mafComp *comp1 = mafAli->components; struct mafComp *comp2 = next->components; printf("<BR><B>Gaps:</B>\n"); for(; comp1 ; comp1 = comp1->next, comp2 = comp2->next) { int diff; char dbOnly[4096]; diff = comp2->start - (comp1->start + comp1->size); safef(dbOnly, sizeof(dbOnly), "%s", comp1->src); chopPrefix(dbOnly); printf("%-20s %d\n",hOrganism(dbOnly), diff); } printf("<BR>"); } } } } char **getIdNameMap(struct trackDb *tdb, struct asColumn *col, int *size) /* Allocate and fill an array mapping id to name. Currently limited to specific columns. */ { char *idNameTable = trackDbSetting(tdb, "sourceTable"); if (!idNameTable || differentString("sourceIds", col->name)) return NULL; struct sqlResult *sr; char query[256]; char **row; char **idNames; sqlSafef(query, sizeof(query), "select max(id) from %s", idNameTable); struct sqlConnection *conn = hAllocConnTrack(database, tdb); int maxId = sqlQuickNum(conn, query); AllocArray(idNames, maxId+1); sqlSafef(query, sizeof(query), "select id, name from %s", idNameTable); sr = sqlGetResult(conn, query); int id; while ((row = sqlNextRow(sr)) != NULL) { id = sqlUnsigned(row[0]); if (id > maxId) errAbort("Internal error: id %d > maxId %d in %s", id, maxId, idNameTable); idNames[id] = cloneString(row[1]); } sqlFreeResult(&sr); hFreeConn(&conn); if (size) *size = maxId+1; return idNames; } void printIdOrLinks(struct asColumn *col, struct hash *fieldToUrl, struct trackDb *tdb, char *idList) /* if trackDb does not contain a "urls" entry for current column name, just print idList as it is. * Otherwise treat idList as a comma-sep list of IDs and print one row per id, with a link to url, * ($$ in url is OK, wildcards like $P, $p, are also OK) * */ { // try to find a fieldName=url setting in the "urls" tdb statement, print id if not found char *url = NULL; if (fieldToUrl != NULL) url = (char*)hashFindVal(fieldToUrl, col->name); if (url == NULL) { printf("<td>%s</td></tr>\n", idList); return; } // split the id into parts and print each part as a link struct slName *slIds = slNameListFromComma(idList); struct slName *itemId = NULL; // handle id->name mapping for multi-source items int nameCount; char **idNames = getIdNameMap(tdb, col, &nameCount); printf("<td>"); for (itemId = slIds; itemId!=NULL; itemId = itemId->next) { if (itemId != slIds) printf(", "); char *itemName = trimSpaces(itemId->name); if (idNames) { unsigned int id = sqlUnsigned(itemName); if (id < nameCount) itemName = idNames[sqlUnsigned(itemName)]; } // a | character can optionally be used to separate the ID used for $$ from the name shown in the link (like in Wikimedia markup) char *idForUrl = itemName; boolean encode = TRUE; if (strstr(itemName, "|")) { char *parts[2]; chopString(itemName, "|", parts, ArraySize(parts)); idForUrl = parts[0]; itemName = parts[1]; encode = FALSE; // assume the link is already encoded } char *idUrl = replaceInUrl(url, idForUrl, cart, database, seqName, winStart, winEnd, tdb->track, encode, NULL); printf("<a href=\"%s\" target=\"_blank\">%s</a>", idUrl, itemName); } printf("</td></tr>\n"); freeMem(slIds); //freeMem(idNames); } int extraFieldsStart(struct trackDb *tdb, int fieldCount, struct asObject *as) /* return the index of the first extra field */ { int start = 0; char *type = cloneString(tdb->type); char *word = nextWord(&type); if (word && (sameWord(word,"bed") || startsWith("big", word))) { if (NULL != (word = nextWord(&type))) start = sqlUnsigned(word); else // custom beds and bigBeds may not have full type "begBed 9 +" start = max(0,slCount(as->columnList) - fieldCount); } return start; } struct slPair *getExtraFields(struct trackDb *tdb, char **fields, int fieldCount) /* return the extra field names and their values as a list of slPairs. */ { struct asObject *as = asForDb(tdb, database); if (as == NULL) return NULL; struct asColumn *col = as->columnList; int start = extraFieldsStart(tdb, fieldCount, as); // skip past known fields for (;start !=0 && col != NULL;col=col->next) if (start > 0) start--; struct slPair *extraFields = 0; int count = 0; for (;col != NULL && count < fieldCount;col=col->next) { struct slPair *slp; AllocVar(slp); char *fieldName = col->name; char *fieldVal = fields[count]; slp->name = fieldName; slp->val = fieldVal; slAddHead(&extraFields, slp); count++; //printf("name %s, val %s, idx %d<br>", fieldName, fieldVal, count); } slReverse(extraFields); return extraFields; } struct slPair *getFields(struct trackDb *tdb, char **row) /* return field names and their values as a list of slPairs. */ // TODO: refactor with getExtraFields { struct asObject *as = asForDb(tdb, database); if (as == NULL) return NULL; int fieldCount = slCount(as->columnList); struct slPair *fields = NULL; struct asColumn *col = as->columnList; int count = 0; for (count = 0; col != NULL && count < fieldCount; col = col->next) { struct slPair *field; AllocVar(field); char *fieldName = col->name; char *fieldVal = row[count]; field->name = fieldName; field->val = fieldVal; slAddHead(&fields, field); count++; } slReverse(fields); return fields; } int extraFieldsPrint(struct trackDb *tdb,struct sqlResult *sr,char **fields,int fieldCount) // Any extra bed or bigBed fields (defined in as and occurring after N in bed N + types. // sr may be null for bigBeds. // Returns number of extra fields actually printed. { struct asObject *as = asForDb(tdb, database); if (as == NULL) return 0; // We are trying to print extra fields so we need to figure out how many fields to skip int start = extraFieldsStart(tdb, fieldCount, as); struct asColumn *col = as->columnList; char *urlsStr = trackDbSettingClosestToHomeOrDefault(tdb, "urls", NULL); struct hash* fieldToUrl = hashFromString(urlsStr); boolean skipEmptyFields = trackDbSettingOn(tdb, "skipEmptyFields"); // make list of fields to skip char *skipFieldsStr = trackDbSetting(tdb, "skipFields"); struct slName *skipIds = NULL; if (skipFieldsStr) skipIds = slNameListFromComma(skipFieldsStr); // make list of fields that are separated from other fields char *sepFieldsStr = trackDbSetting(tdb, "sepFields"); struct slName *sepFields = NULL; if (sepFieldsStr) sepFields = slNameListFromComma(sepFieldsStr); // iterate over fields, print as table rows int count = 0; for (;col != NULL && count < fieldCount;col=col->next) { if (start > 0) // skip past already known fields { start--; continue; } int ix = count; if (sr != NULL) { ix = sqlFieldColumn(sr, col->name); // If sr provided, name must match sql columnn name! if (ix == -1 || ix > fieldCount) // so extraField really just provides a label continue; } char *fieldName = col->name; if (count == 0) printf("<br><table class='bedExtraTbl'>"); count++; // do not print a row if the fieldName from the .as file is in the "skipFields" list // or if a field name starts with _. This maked bigBed extra fields consistent with // external extra fields in that _ field names have some meaning and are not shown if (startsWith("_", fieldName) || (skipIds && slNameInList(skipIds, fieldName))) continue; // skip this row if it's empty and "skipEmptyFields" option is set if (skipEmptyFields && isEmpty(fields[ix])) continue; // split this table to separate current row from the previous one, if the trackDb option is set if (sepFields && slNameInList(sepFields, fieldName)) printf("</tr></table>\n<p>\n<table class='bedExtraTbl'>"); // field description char *entry; if (sameString(fieldName, "cdsStartStat") && sameString("enum('none','unk','incmpl','cmpl')", col->comment)) entry = "Status of CDS start annotation (none, unknown, incomplete, or complete)"; else if (sameString(fieldName, "cdsEndStat") && sameString("enum('none','unk','incmpl','cmpl')", col->comment)) entry = "Status of CDS end annotation (none, unknown, incomplete, or complete)"; else entry = col->comment; printf("<tr><td>%s</td>", entry); // bold style now in HGStyle.css if (col->isList || col->isArray || col->lowType->stringy || asTypesIsInt(col->lowType->type)) printIdOrLinks(col, fieldToUrl, tdb, fields[ix]); else if (asTypesIsFloating(col->lowType->type)) { double valDouble = strtod(fields[ix],NULL); if (errno == 0 && valDouble != 0) printf("<td>%g</td></tr>\n", valDouble); else printf("<td>%s</td></tr>\n", fields[ix]); // decided not to print error } else printf("<td>%s</td></tr>\n", fields[ix]); } asObjectFree(&as); if (skipIds) slFreeList(skipIds); if (sepFields) slFreeList(sepFields); if (count > 0) printf("</table>\n"); return count; } void genericBedClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int bedSize) /* Handle click in generic BED track. */ { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("genericBedClick track %s not found", tdb->table); if (bedSize <= 3) sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d", table, seqName, start); else { struct hTableInfo *hti = hFindTableInfoWithConn(conn, seqName, tdb->table); if (hti && *hti->nameField && differentString("name", hti->nameField)) sqlSafef(query, sizeof query, "select * from %s where %s = '%s' and chrom = '%s' and chromStart = %d", table, hti->nameField, item, seqName, start); else sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); } sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, bedSize); bedPrintPos(bed, bedSize, tdb); extraFieldsPrint(tdb,sr,row,sqlCountColumns(sr)); // check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign) char *setting = trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE); if (bedSize == 6 && setting && sameString(setting, "seq1Seq2")) printf("<br><B>Sequence 1:</B> %s<br><B>Sequence 2:</B> %s<br>\n",row[hasBin+6], row[hasBin+7]); printCompareGenomeLinks(tdb,bed->name); } sqlFreeResult(&sr); getBedTopScorers(conn, tdb, table, item, start, bedSize); printItemDetailsHtml(tdb, item); } #define INTRON 10 #define CODINGA 11 #define CODINGB 12 #define UTR5 13 #define UTR3 14 #define STARTCODON 15 #define STOPCODON 16 #define SPLICESITE 17 #define NONCONSPLICE 18 #define INFRAMESTOP 19 #define INTERGENIC 20 #define REGULATORY 21 #define LABEL 22 #define RED 0xFF0000 #define GREEN 0x00FF00 #define LTGREEN 0x33FF33 #define BLUE 0x0000FF #define MEDBLUE 0x6699FF #define PURPLE 0x9900cc #define BLACK 0x000000 #define CYAN 0x00FFFF #define ORANGE 0xDD6600 #define BROWN 0x663300 #define YELLOW 0xFFFF00 #define MAGENTA 0xFF00FF #define GRAY 0xcccccc #define LTGRAY 0x999999 #define WHITE 0xFFFFFF int setAttributeColor(int class) { switch (class) { case STARTCODON: return GREEN; case STOPCODON: return RED; case CODINGA: return MEDBLUE; case CODINGB: return PURPLE; case UTR5: case UTR3: return ORANGE; case INTRON: return LTGRAY; case SPLICESITE: case NONCONSPLICE: return BLACK; case INFRAMESTOP: return MAGENTA; case REGULATORY: return YELLOW; case INTERGENIC: return GRAY; case LABEL: default: return BLACK; } } void startColorStr(struct dyString *dy, int color, int track) { currentColor[track] = color; if (prevColor[track] != currentColor[track]) dyStringPrintf(dy,"</span><span style='color:#%06X'>",color); } void stopColorStr(struct dyString *dy, int track) { prevColor[track] = currentColor[track]; } void addTag(struct dyString *dy, struct dyString *tag) { dyStringPrintf(dy,"<A name=%s></a>",tag->string); } void setClassStr(struct dyString *dy, int class, int track) { if (class == STARTCODON) dyStringAppend(dy,"<A name=startcodon></a>"); startColorStr(dy,setAttributeColor(class),track); } void resetClassStr(struct dyString *dy, int track) { stopColorStr(dy,track); } boolean isBlue(char *s) /* check for <a href name=class</a> to see if this is colored blue (coding region)*/ { /* check for blue */ if (strstr(s,"6699FF") == NULL) return FALSE; else return TRUE; } int numberOfGaps(char *q,int size) /* count number of gaps in a string array */ { int i; int count = 0; for (i = 0 ; i<size ; i++) if (q[i] == '-') count++; return (count); } void pseudoGeneClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int bedSize) /* Handle click in track. */ { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("pseudoGeneClick track %s not found", tdb->table); if (bedSize <= 3) sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d", table, seqName, start); else sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, bedSize); bedPrintPos(bed, bedSize, tdb); } } void axtOneGeneOut(char *otherDb, struct axt *axtList, int lineSize, FILE *f, struct genePred *gp, char *nibFile) /* Output axt and orf in pretty format. */ { struct axt *axt; int oneSize; int i; int tCodonPos = 1; int qCodonPos = 1; int tStart; int tEnd; int nextStart= gp->exonStarts[0] ; int nextEnd = gp->exonEnds[0]; int nextEndIndex = 0; int tCoding=FALSE; int qCoding=FALSE; int qStopCodon = FALSE; int tFlip=TRUE; /* flag to control target alternating colors for exons (blue and purple) */ int qFlip=TRUE; /* flag to control query alternating colors for exons (blue and purple) */ int qClass=INTERGENIC; int tClass=INTERGENIC; int prevTclass=INTERGENIC; int prevQclass=INTERGENIC; int posStrand; DNA qCodon[4]; DNA tCodon[4]; AA qProt, tProt = 0; int tPtr = 0; int prevEnd = 500000000; int intronTruncated=FALSE; if (gp->strand[0] == '+') { nextEndIndex = 0; nextStart = gp->exonStarts[nextEndIndex] ; nextEnd = gp->exonEnds[nextEndIndex]; tStart = gp->cdsStart ; tEnd = gp->cdsEnd-3 ; posStrand=TRUE; if (axtList != NULL) tPtr = axtList->tStart; } else if (gp->strand[0] == '-') { nextEndIndex = (gp->exonCount)-1; nextStart = (gp->exonEnds[nextEndIndex]); nextEnd = (gp->exonStarts[nextEndIndex]); tStart = gp->cdsEnd ; tEnd = gp->cdsStart ; posStrand=FALSE; if (axtList != NULL) tPtr = axtList->tEnd; } else { errAbort("cannot determine start_codon position for %s on %s\n",gp->name,gp->chrom); exit(0); } /* safef(nibFile, sizeof(nibFile), "%s/%s.nib",nibDir,gp->chrom); */ /* if no alignment , make a bad one */ if (axtList == NULL) { if (gp->strand[0] == '+') axtList = createAxtGap(nibFile,gp->chrom,tStart,tEnd ,gp->strand[0]); else axtList = createAxtGap(nibFile,gp->chrom,tEnd,tStart ,gp->strand[0]); } /* append unaligned coding region to list */ if (posStrand) { if ((axtList->tStart)-1 > tStart) { struct axt *axtGap = createAxtGap(nibFile,gp->chrom,tStart,axtList->tStart,gp->strand[0]); slAddHead(&axtList, axtGap); tPtr = axtList->tStart; } } else { if (axtList->tEnd < tStart) { struct axt *axtGap = createAxtGap(nibFile,gp->chrom,axtList->tEnd, tStart+1,gp->strand[0]); axtListReverse(&axtGap, database); slAddHead(&axtList, axtGap); tPtr = axtList->tEnd; } } for (axt = axtList; axt != NULL; axt = axt->next) { char *q = axt->qSym; char *t = axt->tSym; int size = axt->symCount; int sizeLeft = size; int qPtr ; char qStrand = (axt->qStrand == gp->strand[0] ? '+' : '-'); int qStart = axt->qStart; int qEnd = axt->qEnd; int qSize = 0; if (!sameString(axt->qName, "gap")) qSize = hChromSize(otherDb, axt->qName); if (qStrand == '-') { qStart = qSize - axt->qEnd; qEnd = qSize - axt->qStart; } /* fprintf(f, ">%s:%d-%d %s:%d-%d (%c) score %d coding %d-%d utr/coding %d-%d gene %c alignment %c\n", * axt->tName, axt->tStart+1, axt->tEnd, * axt->qName, qStart+1, qEnd, qStrand, axt->score, tStart+1, tEnd, gp->txStart+1, gp->txEnd, gp->strand[0], axt->qStrand); */ qPtr = qStart; if (gp->exonFrames == NULL) qCodonPos = tCodonPos; /* put translation back in sync */ if (!posStrand) { qPtr = qEnd; /* skip to next exon if we are starting in the middle of a gene - should not happen */ while ((tPtr < nextEnd) && (nextEndIndex > 0)) { nextEndIndex--; prevEnd = nextEnd; nextStart = (gp->exonEnds[nextEndIndex]); nextEnd = (gp->exonStarts[nextEndIndex]); if (nextStart > tStart) tClass = INTRON; } } else { /* skip to next exon if we are starting in the middle of a gene - should not happen */ while ((tPtr > nextEnd) && (nextEndIndex < gp->exonCount-2)) { nextEndIndex++; prevEnd = nextEnd; nextStart = gp->exonStarts[nextEndIndex]; nextEnd = gp->exonEnds[nextEndIndex]; if (nextStart > tStart) tClass = INTRON; } } /* loop thru one base at a time */ while (sizeLeft > 0) { struct dyString *dyT = newDyString(1024); struct dyString *dyQ = newDyString(1024); struct dyString *dyQprot = newDyString(1024); struct dyString *dyTprot = newDyString(1024); struct dyString *exonTag = newDyString(1024); oneSize = sizeLeft; if (oneSize > lineSize) oneSize = lineSize; setClassStr(dyT,tClass, 0); setClassStr(dyQ,qClass, 1); /* break up into linesize chunks */ for (i=0; i<oneSize; ++i) { if (posStrand) {/*look for start of exon on positive strand*/ if ((tClass==INTRON) && (tPtr >= nextStart) && (tPtr >= tStart) && (tPtr < tEnd)) { tCoding=TRUE; dyStringPrintf(exonTag, "exon%d",nextEndIndex+1); addTag(dyT,exonTag); if (gp->exonFrames != NULL && gp->exonFrames[nextEndIndex] != -1) tCodonPos = gp->exonFrames[nextEndIndex]+1; if (qStopCodon == FALSE) { qCoding=TRUE; qCodonPos = tCodonPos; /* put translation back in sync */ qFlip = tFlip; } } else if ((tPtr >= nextStart) && (tPtr < tStart)) { /* start of UTR 5'*/ tClass=UTR5; qClass=UTR5; } } else{ if ((tClass==INTRON) && (tPtr <= nextStart) && (tPtr <= tStart) && (tPtr > tEnd)) { /*look for start of exon on neg strand */ tCoding=TRUE; dyStringPrintf(exonTag, "exon%d",nextEndIndex+1); addTag(dyT,exonTag); if (qStopCodon == FALSE) { qCoding=TRUE; if (gp->exonFrames != NULL && gp->exonFrames[nextEndIndex] != -1) tCodonPos = gp->exonFrames[nextEndIndex]+1; qCodonPos = tCodonPos; /* put translation back in sync */ qFlip = tFlip; } } else if ((tPtr <= nextStart-1) && (tPtr > tStart)) { /* start of UTR 5'*/ tClass=UTR5; qClass=UTR5; } } /* toggle between blue / purple color for exons */ if (tCoding && tFlip ) tClass=CODINGA; if (tCoding && (tFlip == FALSE) ) tClass=CODINGB; if (qCoding && qFlip && !qStopCodon) qClass=CODINGA; if (qCoding && (qFlip == FALSE) && !qStopCodon) qClass=CODINGB; if (posStrand) { /* look for end of exon */ if (tPtr == nextEnd) { tCoding=FALSE; qCoding=FALSE; tClass=INTRON; qClass=INTRON; nextEndIndex++; nextStart = gp->exonStarts[nextEndIndex]; prevEnd = nextEnd; nextEnd = gp->exonEnds[nextEndIndex]; if (gp->exonFrames != NULL && gp->exonFrames[nextEndIndex] != -1) tCodonPos = gp->exonFrames[nextEndIndex]+1; } } else { /* look for end of exon negative strand */ if (tPtr == nextEnd && tPtr != tEnd) { tCoding=FALSE; qCoding=FALSE; tClass=INTRON; qClass=INTRON; nextEndIndex--; nextStart = (gp->exonEnds[nextEndIndex]); prevEnd = nextEnd; nextEnd = (gp->exonStarts[nextEndIndex]); } } if (posStrand) { /* look for start codon and color it green*/ if ((tPtr >= (tStart)) && (tPtr <=(tStart+2))) { if (gp->exonFrames != NULL && gp->cdsStartStat == cdsComplete) { tClass=STARTCODON; qClass=STARTCODON; } else if(tClass != CODINGB) { tClass=CODINGA; qClass=CODINGA; } tCoding=TRUE; qCoding=TRUE; if (tPtr == tStart) { if (gp->exonFrames != NULL && gp->exonFrames[nextEndIndex] != -1) tCodonPos = gp->exonFrames[nextEndIndex]+1; else tCodonPos=1; qCodonPos=tCodonPos; } } /* look for stop codon and color it red */ if ((tPtr >= tEnd) && (tPtr <= (tEnd+2))) { if (gp->exonFrames != NULL && gp->cdsEndStat == cdsComplete) { tClass=STOPCODON; qClass=STOPCODON; } tCoding=FALSE; qCoding=FALSE; } } else { /* look for start codon and color it green negative strand case*/ if ((tPtr <= (tStart)) && (tPtr >=(tStart-2))) { if (gp->exonFrames != NULL && gp->cdsStartStat == cdsComplete) { tClass=STARTCODON; qClass=STARTCODON; } else if (tClass!=CODINGB) { tClass=CODINGA; qClass=CODINGA; } tCoding=TRUE; qCoding=TRUE; if (tPtr == tStart) { if (gp->exonFrames != NULL && gp->exonFrames[nextEndIndex] != -1) tCodonPos = gp->exonFrames[nextEndIndex]+1; else tCodonPos=1; } qCodonPos=tCodonPos; } /* look for stop codon and color it red - negative strand*/ if ((tPtr <= tEnd+3) && (tPtr >= (tEnd+1))) { if (gp->exonFrames != NULL && gp->cdsEndStat == cdsComplete) { tClass=STOPCODON; qClass=STOPCODON; } tCoding=FALSE; qCoding=FALSE; } } if (posStrand) { /* look for 3' utr and color it orange */ if (tPtr == (tEnd +3) ) { tClass = UTR3; qClass = UTR3; } } else { /* look for 3' utr and color it orange negative strand case*/ if (tPtr == (tEnd) ) { tClass = UTR3; qClass = UTR3; } } if (qCoding && qCodonPos == 3) { /* look for in frame stop codon and color it magenta */ qCodon[qCodonPos-1] = q[i]; qCodon[3] = 0; qProt = lookupCodon(qCodon); if (qProt == 'X') qProt = ' '; if (qProt == 0) { qProt = '*'; /* stop codon is * */ qClass = INFRAMESTOP; } } /* write html to change color for all above cases t strand */ if (tClass != prevTclass) { setClassStr(dyT,tClass,0); prevTclass = tClass; } dyStringAppendC(dyT,t[i]); /* write html to change color for all above cases q strand */ if (qClass != prevQclass) { setClassStr(dyQ,qClass,0); prevQclass = qClass; } dyStringAppendC(dyQ,q[i]); if (tCoding && tFlip && (tCodonPos == 3)) { tFlip=FALSE; } else if (tCoding && (tFlip == FALSE) && (tCodonPos == 3)) { tFlip=TRUE; } if (qCoding && qFlip && (qCodonPos == 3)) { qFlip=FALSE; } else if (qCoding && (qFlip == FALSE) && (qCodonPos == 3)) { qFlip=TRUE; } /* translate dna to protein and append html */ if (tCoding && tCodonPos == 3) { tCodon[tCodonPos-1] = t[i]; tCodon[3] = 0; tProt = lookupCodon(tCodon); if (tProt == 'X') tProt = ' '; if (tProt == 0) tProt = '*'; /* stop codon is * */ dyStringAppendC(dyTprot,tProt); } else { dyStringAppendC(dyTprot,' '); } if (qCoding && qCodonPos == 3) { qCodon[qCodonPos-1] = q[i]; qCodon[3] = 0; qProt = lookupCodon(qCodon); if (qProt == 'X') qProt = ' '; if (qProt == 0) { qProt = '*'; /* stop codon is * */ /* qClass = INFRAMESTOP; */ qStopCodon = FALSE; qCoding = TRUE; } if (tProt == qProt) qProt = '|'; /* if the AA matches print | */ dyStringAppendC(dyQprot,qProt); } else { dyStringAppendC(dyQprot,' '); } /* move to next base and update reading frame */ if (t[i] != '-') { if (posStrand) { tPtr++; qPtr++; } else { tPtr--; qPtr--; } if (tCoding) { tCodon[tCodonPos-1] = t[i]; tCodonPos++; } if (tCodonPos>3) tCodonPos=1; } /*else { tClass=INTRON; }*/ /* update reading frame on other species */ if (q[i] != '-') { if (qCoding) { qCodon[qCodonPos-1] = q[i]; qCodonPos++; } if (qCodonPos>3) qCodonPos=1; } /*else { qClass=INTRON; }*/ } /* write labels in black */ resetClassStr(dyT,0); setClassStr(dyT,LABEL,0); if (posStrand) { dyStringPrintf(dyT, " %d ",tPtr); if (tCoding) dyStringPrintf(dyT, "exon %d",(nextEndIndex == 0) ? 1 : nextEndIndex+1); } else { dyStringPrintf(dyT, " %d ",tPtr+1); if (tCoding) dyStringPrintf(dyT, "exon %d", (nextEndIndex == 0) ? 1 : nextEndIndex+1); } #if 0 /* debug version */ if (posStrand) dyStringPrintf(dyT, " %d thisExon=%d-%d xon %d",tPtr, gp->exonStarts[(nextEndIndex == 0) ? 0 : nextEndIndex - 1]+1, gp->exonEnds[(nextEndIndex == 0) ? 0 : nextEndIndex - 1],(nextEndIndex == 0) ? 1 : nextEndIndex); else dyStringPrintf(dyT, " %d thisExon=%d-%d xon %d",tPtr, gp->exonStarts[(nextEndIndex == gp->exonCount) ? gp->exonCount : nextEndIndex ]+1, gp->exonEnds[(nextEndIndex == gp->exonCount) ? gp->exonCount : nextEndIndex ],(nextEndIndex == 0) ? 1 : nextEndIndex); #endif dyStringAppendC(dyT,'\n'); resetClassStr(dyT,0); resetClassStr(dyQ,1); setClassStr(dyQ,LABEL,1); if (posStrand) dyStringPrintf(dyQ, " %d ",qPtr); else dyStringPrintf(dyQ, " %d ",qPtr); dyStringAppendC(dyQ,'\n'); resetClassStr(dyQ,1); dyStringAppendC(dyQprot,'\n'); dyStringAppendC(dyTprot,'\n'); #if 0 /* debug version */ if (posStrand) printf(" %d nextExon=%d-%d xon %d t %d prevEnd %d diffs %d %d<br>",qPtr, nextStart+1,nextEnd,nextEndIndex+1, tPtr,prevEnd, tPtr-nextStart-70, tPtr-(prevEnd+70)); else printf(" %d nextExon=%d-%d xon %d t %d prevEnd %d diffs %d %d<br>",qPtr, nextStart+1,nextEnd,nextEndIndex, tPtr, prevEnd, tPtr-nextStart-70, tPtr-(prevEnd+70)); #endif /* write out alignment, unless we are deep inside an intron */ if (tClass != INTRON || (tClass == INTRON && tPtr < nextStart-LINESIZE && tPtr< (prevEnd + posStrand ? LINESIZE : -LINESIZE))) { intronTruncated = 0; fputs(dyTprot->string,f); fputs(dyT->string,f); for (i=0; i<oneSize; ++i) { if (toupper(q[i]) == toupper(t[i]) && isalpha(q[i])) fputc('|', f); else fputc(' ', f); } fputc('\n', f); fputs(dyQ->string,f); fputs(dyQprot->string,f); fputc('\n', f); } else { if (!(intronTruncated == TRUE)) { printf("...intron truncated...<br>"); intronTruncated = TRUE; } } /* look for end of line */ if (oneSize > lineSize) oneSize = lineSize; sizeLeft -= oneSize; q += oneSize; t += oneSize; freeDyString(&dyT); freeDyString(&dyQ); freeDyString(&dyQprot); freeDyString(&dyTprot); } } } struct axt *getAxtListForGene(struct genePred *gp, char *nib, char *fromDb, char *toDb, struct lineFile *lf) /* get all axts for a gene */ { struct axt *axt, *axtGap; struct axt *axtList = NULL; int prevEnd = gp->txStart; // int prevStart = gp->txEnd; unused variable int tmp; while ((axt = axtRead(lf)) != NULL) { if (sameString(gp->chrom, axt->tName) && ( ( (axt->tStart <= gp->cdsStart && axt->tEnd >= gp->cdsStart) || (axt->tStart <= gp->cdsEnd && axt->tEnd >= gp->cdsEnd ) ) || ( axt->tStart < gp->cdsEnd && axt->tEnd > gp->cdsStart ) ) ) { if (gp->strand[0] == '-') { reverseComplement(axt->qSym, axt->symCount); reverseComplement(axt->tSym, axt->symCount); tmp = hChromSize(fromDb, axt->qName) - axt->qStart; axt->qStart = hChromSize(fromDb, axt->qName) - axt->qEnd; axt->qEnd = tmp; if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart),gp->strand[0]); reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); slAddHead(&axtList, axtGap); } } else if (prevEnd < (axt->tStart)) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart),gp->strand[0]); slAddHead(&axtList, axtGap); } slAddHead(&axtList, axt); prevEnd = axt->tEnd; // prevStart = axt->tStart; unused variable } if (sameString(gp->chrom, axt->tName) && (axt->tStart > gp->txEnd)) { if ((prevEnd < axt->tStart) && prevEnd < min(gp->txEnd, axt->tStart)) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,min(axt->tStart,gp->txEnd),gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } else if (axtList == NULL) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,gp->txEnd,gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } break; } } if (gp->strand[0] == '+') slReverse(&axtList); return axtList ; } struct axt *getAxtListForRange(struct genePred *gp, char *nib, char *fromDb, char *toDb, char *alignment, char *qChrom, int qStart, int qEnd) /* get all axts for a chain */ { struct lineFile *lf ; struct axt *axt, *axtGap; struct axt *axtList = NULL; int prevEnd = gp->txStart; // int prevStart = gp->txEnd; unused variable int tmp; lf = lineFileOpen(getAxtFileName(gp->chrom, toDb, alignment, fromDb), TRUE); printf("file %s\n",lf->fileName); while ((axt = axtRead(lf)) != NULL) { /* if (sameString(gp->chrom , axt->tName)) * printf("axt %s qstart %d axt tStart %d\n",axt->qName, axt->qStart,axt->tStart); */ if ( sameString(gp->chrom, axt->tName) && sameString( qChrom, axt->qName) && positiveRangeIntersection( qStart, qEnd, axt->qStart, axt->qEnd) && positiveRangeIntersection(gp->txStart, gp->txEnd, axt->tStart, axt->tEnd) ) { if (gp->strand[0] == '-') { reverseComplement(axt->qSym, axt->symCount); reverseComplement(axt->tSym, axt->symCount); tmp = hChromSize(fromDb, axt->qName) - axt->qStart; axt->qStart = hChromSize(fromDb, axt->qName) - axt->qEnd; axt->qEnd = tmp; if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart)-1,gp->strand[0]); reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); slAddHead(&axtList, axtGap); } } else if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart)-1,gp->strand[0]); slAddHead(&axtList, axtGap); } slAddHead(&axtList, axt); prevEnd = axt->tEnd; // prevStart = axt->tStart; unused variable } if (sameString(gp->chrom, axt->tName) && (axt->tStart > gp->txEnd+20000)) { if (axt->tStart > prevEnd) { axtGap = createAxtGap(nib,gp->chrom,prevEnd+1,(axt->tStart)-1,gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } break; } } if (gp->strand[0] == '+') slReverse(&axtList); return axtList ; } void printCdsStatus(enum cdsStatus cdsStatus) /* print a description of a genePred cds status */ { switch (cdsStatus) { case cdsNone: /* "none" - No CDS (non-coding) */ printf("none (non-coding)<br>\n"); break; case cdsUnknown: /* "unk" - CDS is unknown (coding, but not known) */ printf("unknown (coding, but not known)<br>\n"); break; case cdsIncomplete: /* "incmpl" - CDS is not complete at this end */ printf("<em>not</em> complete<br>\n"); break; case cdsComplete: /* "cmpl" - CDS is complete at this end */ printf("complete<br>\n"); break; } } void showGenePos(char *name, struct trackDb *tdb) /* Show gene prediction position and other info. */ { char *rootTable = tdb->table; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct genePred *gpList = NULL, *gp = NULL; char table[HDB_MAX_TABLE_STRING]; struct sqlResult *sr = NULL; char **row = NULL; char *classTable = trackDbSetting(tdb, GENEPRED_CLASS_TBL); if (!hFindSplitTable(database, seqName, rootTable, table, sizeof table, NULL)) errAbort("showGenePos track %s not found", rootTable); sqlSafefFrag(query, sizeof(query), "name = \"%s\"", name); gpList = genePredReaderLoadQuery(conn, table, query); for (gp = gpList; gp != NULL; gp = gp->next) { printPos(gp->chrom, gp->txStart, gp->txEnd, gp->strand, FALSE, NULL); if(sameString(tdb->type,"genePred") && startsWith("ENCODE Gencode",tdb->longLabel) && startsWith("ENST",name)) { char *ensemblIdUrl = trackDbSetting(tdb, "ensemblIdUrl"); printf("<b>Ensembl Transcript Id: </b>"); if (ensemblIdUrl != NULL) printf("<a href=\"%s%s\" target=\"_blank\">%s</a><br>", ensemblIdUrl,name,name); else printf("%s<br>",name); } if (gp->name2 != NULL && strlen(trimSpaces(gp->name2))> 0) { /* in Ensembl gene info downloaded from ftp site, sometimes the name2 field is populated with "noXref" because there is no alternate name. Replace this with "none" */ printf("<b>Gene Symbol:"); if ((strlen(gp->name2) < 1) || (sameString(gp->name2, "noXref"))) printf("</b> none<br>\n"); else printf("</b> %s<br>\n",gp->name2); } char *ensemblSource = NULL; if (sameString("ensGene", table)) { if (hTableExists(database, "ensemblSource")) { sqlSafef(query, sizeof(query), "select source from ensemblSource where name='%s'", name); ensemblSource = sqlQuickString(conn, query); } } if ((gp->exonFrames != NULL) && (!genbankIsRefSeqNonCodingMRnaAcc(gp->name))) { if (ensemblSource && differentString("protein_coding",ensemblSource)) { printf("<b>CDS Start: </b> none (non-coding)<BR>\n"); printf("<b>CDS End: </b> none (non-coding)<BR>\n"); } else { printf("<b>CDS Start: </b>"); printCdsStatus((gp->strand[0] == '+') ? gp->cdsStartStat : gp->cdsEndStat); printf("<b>CDS End: </b>"); printCdsStatus((gp->strand[0] == '+') ? gp->cdsEndStat : gp->cdsStartStat); } } /* if a gene class table exists, get gene class and print */ if (classTable != NULL) { if (hTableExists(database, classTable)) { sqlSafef(query, sizeof(query), "select class from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); /* print class */ if ((row = sqlNextRow(sr)) != NULL) printf("<b>Prediction Class:</b> %s<br>\n", row[0]); sqlFreeResult(&sr); if (sqlFieldIndex(conn, classTable, "level") > 0 ) { sqlSafef(query, sizeof(query), "select level from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("<b>Level: </b> %s<br>\n", row[0]); sqlFreeResult(&sr); } if (sqlFieldIndex(conn, classTable, "transcriptType") > 0 ) { sqlSafef(query, sizeof(query), "select transcriptType from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("<b>Transcript type: </b> %s<br>\n", row[0]); sqlFreeResult(&sr); } if (sqlFieldIndex(conn, classTable, "geneDesc") > 0 ) { sqlSafef(query, sizeof(query), "select geneDesc from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) if (differentString("NULL",row[0])) printf("<b>Gene Description :</b> %s<br>\n", row[0]); sqlFreeResult(&sr); } if (sqlFieldIndex(conn, classTable, "type") > 0 ) { sqlSafef(query, sizeof(query), "select type from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) if (differentString("NULL",row[0])) printf("<b>Gene Type :</b> %s<br>\n", row[0]); } } } if (gp->next != NULL) printf("<br>"); } genePredFreeList(&gpList); sqlFreeResult(&sr); hFreeConn(&conn); } void showGenePosMouse(char *name, struct trackDb *tdb, struct sqlConnection *connMm) /* Show gene prediction position and other info. */ { char query[512]; char *rootTable = tdb->table; struct sqlResult *sr; char **row; struct genePred *gp = NULL; boolean hasBin; int posCount = 0; char table[HDB_MAX_TABLE_STRING]; if (!hFindSplitTable(database, seqName, rootTable, table, sizeof table, &hasBin)) errAbort("showGenePosMouse track %s not found", rootTable); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", table, name); sr = sqlGetResult(connMm, query); while ((row = sqlNextRow(sr)) != NULL) { if (posCount > 0) printf("<BR>\n"); ++posCount; gp = genePredLoad(row + hasBin); printPos(gp->chrom, gp->txStart, gp->txEnd, gp->strand, FALSE, NULL); genePredFree(&gp); } sqlFreeResult(&sr); } void linkToPal(char *track, char *chrom, int start, int end, char *geneName) /* Make anchor tag to open pal window */ { printf("<A TITLE=\"%s\" HREF=\"%s?g=%s&i=%s&c=%s&l=%d&r=%d\">", geneName, hgPalName(), track, geneName, chrom, start, end); printf("CDS FASTA alignment</A> from multiple alignment"); } void addPalLink(struct sqlConnection *conn, char *track, char *chrom, int start, int end, char *geneName) { struct slName *list = hTrackTablesOfType(conn, "wigMaf%%"); if (list != NULL) { puts("<LI>\n"); linkToPal( track, chrom, start, end, geneName); puts("</LI>\n"); } } void geneShowPosAndLinksPal(char *geneName, char *pepName, struct trackDb *tdb, char *pepTable, char *pepClick, char *mrnaClick, char *genomicClick, char *mrnaDescription, struct palInfo *palInfo) /* Show parts of gene common to everything. If pepTable is not null, * it's the old table name, but will check gbSeq first. */ { char *geneTable = tdb->table; boolean foundPep = FALSE; showGenePos(geneName, tdb); if (startsWith("ENCODE Gencode",tdb->longLabel)) { char *yaleTable = trackDbSetting(tdb, "yalePseudoAssoc"); if ((yaleTable != NULL) && (hTableExists(database, yaleTable))) { struct sqlConnection *conn = hAllocConn(database); char query[512]; sqlSafef(query, sizeof(query), "select * from %s where transcript = '%s'", yaleTable, geneName); char buffer[512]; struct sqlResult *sr = sqlGetResult(conn, query); char *yaleUrl = trackDbSetting(tdb, "yaleUrl"); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct yaleGencodeAssoc *ya = yaleGencodeAssocLoad(row); safef(buffer, sizeof buffer, "%s/%s",yaleUrl,ya->yaleId); printf("<B>Yale pseudogene:</B> <a href=\"%s\" target=\"_blank\">%s</a><br>\n", buffer, ya->yaleId); } sqlFreeResult(&sr); hFreeConn(&conn); } } printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); if ((pepTable != NULL) && hGenBankHaveSeq(database, pepName, pepTable)) { puts("<LI>\n"); hgcAnchorSomewhere(pepClick, pepName, pepTable, seqName); printf("Predicted Protein</A> \n"); puts("</LI>\n"); foundPep = TRUE; } if (!foundPep) { char *autoTranslate = trackDbSetting(tdb, "autoTranslate"); if (autoTranslate == NULL || differentString(autoTranslate, "0")) { puts("<LI>\n"); /* put out correct message to describe translated mRNA */ if ( sameString(geneTable, "ensGene") || sameString(geneTable, "ws245Genes") || sameString(geneTable, "vegaGene") || sameString(geneTable, "vegaPseudoGene") || genbankIsRefSeqNonCodingMRnaAcc(geneName) || sameString(geneTable, "lincRNAsTranscripts") ) { printf("Non-protein coding gene or gene fragment, no protein prediction available."); } else { hgcAnchorSomewhere("htcTranslatedPredMRna", geneName, "translate", seqName); printf("Translated Protein</A> from "); if (sameString(geneTable, "refGene") ) { printf("genomic DNA\n"); } else { printf("predicted mRNA \n"); } foundPep = TRUE; } puts("</LI>\n"); } } puts("<LI>\n"); hgcAnchorSomewhere(mrnaClick, geneName, geneTable, seqName); /* hack to put out a correct message describing the mRNA */ if (sameString(mrnaClick, "htcGeneMrna")) printf("%s</A> from genomic sequences\n", mrnaDescription); else printf("%s</A> (may be different from the genomic sequence)\n", mrnaDescription); puts("</LI>\n"); puts("<LI>\n"); hgcAnchorSomewhere(genomicClick, geneName, geneTable, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); if (palInfo) { struct sqlConnection *conn = hAllocConn(database); addPalLink(conn, tdb->track, palInfo->chrom, palInfo->left, palInfo->right, palInfo->rnaName); hFreeConn(&conn); } printf("</UL>\n"); } void geneShowPosAndLinks(char *geneName, char *pepName, struct trackDb *tdb, char *pepTable, char *pepClick, char *mrnaClick, char *genomicClick, char *mrnaDescription) { geneShowPosAndLinksPal(geneName, pepName, tdb, pepTable, pepClick, mrnaClick, genomicClick, mrnaDescription, NULL); } void geneShowPosAndLinksDNARefseq(char *geneName, char *pepName, struct trackDb *tdb, char *pepTable, char *pepClick, char *mrnaClick, char *genomicClick, char *mrnaDescription) /* Show parts of a DNA based RefSeq gene */ { char *geneTable = tdb->table; showGenePos(geneName, tdb); printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); puts("<LI>\n"); hgcAnchorSomewhere(genomicClick, geneName, geneTable, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); printf("</UL>\n"); } void geneShowPosAndLinksMouse(char *geneName, char *pepName, struct trackDb *tdb, char *pepTable, struct sqlConnection *connMm, char *pepClick, char *mrnaClick, char *genomicClick, char *mrnaDescription) /* Show parts of gene common to everything */ { char *geneTrack = tdb->track; showGenePosMouse(geneName, tdb, connMm); printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); if (pepTable != NULL && hTableExists(database, pepTable)) { hgcAnchorSomewhereDb(pepClick, pepName, pepTable, seqName, mousedb); printf("<LI>Translated Protein</A> \n"); } hgcAnchorSomewhereDb(mrnaClick, geneName, geneTrack, seqName, mousedb); printf("<LI>%s</A>\n", mrnaDescription); hgcAnchorSomewhereDb(genomicClick, geneName, geneTrack, seqName, mousedb); printf("<LI>Genomic Sequence</A> DNA sequence from assembly\n"); printf("</UL>\n"); } void geneShowCommon(char *geneName, struct trackDb *tdb, char *pepTable) /* Show parts of gene common to everything */ { geneShowPosAndLinks(geneName, geneName, tdb, pepTable, "htcTranslatedProtein", "htcGeneMrna", "htcGeneInGenome", "Predicted mRNA"); char *txInfo = trackDbSetting(tdb, "txInfo"); if (txInfo != NULL) showTxInfo(geneName, tdb, txInfo); char *cdsEvidence = trackDbSetting(tdb, "cdsEvidence"); if (cdsEvidence != NULL) showCdsEvidence(geneName, tdb, cdsEvidence); } void geneShowMouse(char *geneName, struct trackDb *tdb, char *pepTable, struct sqlConnection *connMm) /* Show parts of gene common to everything */ { geneShowPosAndLinksMouse(geneName, geneName, tdb, pepTable, connMm, "htcTranslatedProtein", "htcGeneMrna", "htcGeneInGenome", "Predicted mRNA"); } void genericGenePredClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *pepTable, char *mrnaTable) /* Handle click in generic genePred track. */ { char *oldToNew = trackDbSetting(tdb, "oldToNew"); if (oldToNew != NULL && sqlTableExists(conn, oldToNew)) { char query[512]; sqlSafef(query, sizeof(query), "select * from %s where oldId = '%s' and oldChrom='%s' and oldStart=%d", oldToNew, item, seqName, start); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct kg1ToKg2 *x = kg1ToKg2Load(row); printf("<B>Old ID:</B> %s<BR>\n", x->oldId); printf("<B>New ID:</B> %s<BR>\n", naForEmpty(x->newId)); printf("<B>Old/New Mapping:</B> %s<BR>\n", x->status); if (x->note[0] != 0) printf("<B>Notes:</B> %s<BR>\n", x->note); printf("<BR>\n"); } sqlFreeResult(&sr); } geneShowCommon(item, tdb, pepTable); printItemDetailsHtml(tdb, item); } void pslDumpHtml(struct psl *pslList) /* print out psl header and data */ { struct psl* psl; printf("<PRE><TT>\n"); printf("#match\tmisMatches\trepMatches\tnCount\tqNumInsert\tqBaseInsert\ttNumInsert\tBaseInsert\tstrand\tqName\tqSize\tqStart\tqEnd\ttName\ttSize\ttStart\ttEnd\tblockCount\tblockSizes\tqStarts\ttStarts\n"); for (psl = pslList; psl != NULL; psl = psl->next) { pslTabOut(psl, stdout); } printf("</TT></PRE>\n"); } void genericBigPslClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end) /* Handle click in big psl track. */ { struct psl* pslList = NULL; char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); struct bbiFile *bbi = bigBedFileOpen(fileName); struct lm *lm = lmInit(0); int ivStart = start, ivEnd = end; if (start == end) { // item is an insertion; expand the search range from 0 bases to 2 so we catch it: ivStart = max(0, start-1); ivEnd++; } boolean showEvery = sameString(item, "PrintAllSequences"); boolean showAll = trackDbSettingOn(tdb, "showAll"); unsigned seqTypeField = bbExtraFieldIndex(bbi, "seqType"); struct bigBedInterval *bb, *bbList = NULL; // If showAll is on, show all alignments with this qName, not just the // selected one. if (showEvery) { struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi); for (chrom = chromList; chrom != NULL; chrom = chrom->next) { char *chromName = chrom->name; int start = 0, end = chrom->size; int itemsLeft = 0; // Zero actually means no limit.... struct bigBedInterval *intervalList = bigBedIntervalQuery(bbi, chromName, start, end, itemsLeft, lm); slCat(&bbList, intervalList); } } else if (showAll) { int fieldIx; struct bptFile *bpt = bigBedOpenExtraIndex(bbi, "name", &fieldIx); bbList = bigBedNameQuery(bbi, bpt, fieldIx, item, lm); } else bbList = bigBedIntervalQuery(bbi, seqName, ivStart, ivEnd, 0, lm); /* print out extra fields */ for (bb = bbList; bb != NULL; bb = bb->next) { char *restFields[256]; int restCount = chopTabs(cloneString(bb->rest), restFields); if (sameString(restFields[0], item)) { int bedSize = 25; int restBedFields = bedSize - 3; if (restCount > restBedFields) { char **extraFields = (restFields + restBedFields); int extraFieldCount = restCount - restBedFields; int printCount = extraFieldsPrint(tdb,NULL,extraFields, extraFieldCount); printCount += 0; } } } char *bedRow[32]; char startBuf[16], endBuf[16]; int lastChromId = -1; char chromName[bbi->chromBpt->keySize+1]; for (bb = bbList; bb != NULL; bb = bb->next) { bbiCachedChromLookup(bbi, bb->chromId, lastChromId, chromName, sizeof(chromName)); lastChromId=bb->chromId; bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, 4); if (showEvery || sameString(bedRow[3], item)) { struct psl *psl= pslFromBigPsl(chromName, bb, seqTypeField, NULL, NULL); slAddHead(&pslList, psl); } } char *sort = cartUsualString(cart, "sort", pslSortList[0]); pslSortListByVar(&pslList, sort); if (showEvery) printf("<H3>Genomic Alignments</H3>"); else printf("<H3>%s/Genomic Alignments</H3>", item); if (showEvery || pslIsProtein(pslList)) printAlignmentsSimple(pslList, start, "htcBigPslAli", tdb->table, item); else printAlignmentsExtra(pslList, start, "htcBigPslAli", "htcBigPslAliInWindow", tdb->table, item); pslFreeList(&pslList); printItemDetailsHtml(tdb, item); } void genericPslClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *subType) /* Handle click in generic psl track. */ { struct psl* pslList = getAlignments(conn, tdb->table, item); /* check if there is an alignment available for this sequence. This checks * both genbank sequences and other sequences in the seq table. If so, * set it up so they can click through to the alignment. */ if (hGenBankHaveSeq(database, item, NULL)) { printf("<H3>%s/Genomic Alignments</H3>", item); if (sameString("protein", subType)) printAlignments(pslList, start, "htcProteinAli", tdb->table, item); else printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); } else { /* just dump the psls */ pslDumpHtml(pslList); } pslFreeList(&pslList); printItemDetailsHtml(tdb, item); } static char *getParentTableName(struct trackDb *tdb) /* Get the track table or composite track parent table if applicable. */ { tdb = trackDbTopLevelSelfOrParent(tdb); return tdb->table; } static char *getParentTrackName(struct trackDb *tdb) /* Get the track name or composite track parent name if applicable. */ { tdb = trackDbTopLevelSelfOrParent(tdb); return tdb->track; } void printTBSchemaLink(struct trackDb *tdb) /* Make link to TB schema -- unless this is an on-the-fly (tableless) track. */ { if (hTableOrSplitExists(database, tdb->table)) { char *trackTable = getParentTableName(tdb); printf("<P><A HREF=\"../cgi-bin/hgTables?db=%s&hgta_group=%s&hgta_track=%s" "&hgta_table=%s&position=%s:%d-%d&" "hgta_doSchema=describe+table+schema\" target=ucscSchema title='Open schema in new window'>" "View table schema</A></P>\n", database, tdb->grp, trackTable, tdb->table, seqName, winStart+1, winEnd); } } void printTrackUiLink(struct trackDb *tdb) /* Make link to hgTrackUi. */ { char *trackName = getParentTrackName(tdb); struct trackDb *parentTdb = tdb; if (!sameString(trackName, tdb->track)) parentTdb = hTrackDbForTrack(database, trackName); printf("<P><A HREF=\"%s?g=%s&%s\">" "Go to %s track controls</A></P>\n", hTrackUiForTrack(tdb->track), trackName, cartSidUrlString(cart), parentTdb->shortLabel); } void printDataRestrictionDate(struct trackDb *tdb) /* If this annotation has a dateUnrestricted trackDb setting, print it */ { char *restrictionDate = encodeRestrictionDateDisplay(database,tdb); if (restrictionDate != NULL) { printf("<A HREF=\"/ENCODE/terms.html\" TARGET=_BLANK><B>Restricted until</A>:</B> %s <BR>\n", restrictionDate); freeMem(restrictionDate); } } static void printOrigAssembly(struct trackDb *tdb) /* If this annotation has been lifted, print the original * freeze, as indicated by the "origAssembly" trackDb setting */ { trackDbPrintOrigAssembly(tdb, database); } static char *getHtmlFromSelfOrParent(struct trackDb *tdb) /* Get html from self or from parent if not in self. */ { for (;tdb != NULL; tdb = tdb->parent) { if (tdb->html != NULL && tdb->html[0] != 0) return tdb->html; } return NULL; } void printTrackHtml(struct trackDb *tdb) /* If there's some html associated with track print it out. Also print * last update time for data table and make a link * to the TB table schema page for this table. */ { if (!isCustomTrack(tdb->track)) { extraUiLinks(database, tdb); printTrackUiLink(tdb); printOrigAssembly(tdb); printDataVersion(database, tdb); printUpdateTime(database, tdb, NULL); printDataRestrictionDate(tdb); } char *html = getHtmlFromSelfOrParent(tdb); if (html != NULL && html[0] != 0) { htmlHorizontalLine(); // Add pennantIcon printPennantIconNote(tdb); // Wrap description html in div with limited width, so when the page is very wide // due to long details, the user doesn't have to scroll right to read the description. puts("<div class='readableWidth'>"); puts(html); puts("</div>"); } hPrintf("<BR>\n"); } void qChainRangePlusStrand(struct chain *chain, int *retQs, int *retQe) /* Return range of bases covered by chain on q side on the plus * strand. */ { if (chain == NULL) errAbort("Can't find range in null query chain."); if (chain->qStrand == '-') { *retQs = chain->qSize - chain->qEnd+1; *retQe = chain->qSize - chain->qStart; } else { *retQs = chain->qStart+1; *retQe = chain->qEnd; } } struct chain *chainDbLoad(struct sqlConnection *conn, char *db, char *track, char *chrom, int id) /* Load chain. */ { char table[HDB_MAX_TABLE_STRING]; char query[256]; struct sqlResult *sr; char **row; boolean hasBin; struct chain *chain; if (!hFindSplitTable(db, seqName, track, table, sizeof table, &hasBin)) errAbort("No %s track in database %s for %s", track, db, seqName); sqlSafef(query, sizeof(query), "select * from %s where id = %d", table, id); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) errAbort("Can't find %d in %s", id, table); chain = chainHeadLoad(row + hasBin); sqlFreeResult(&sr); chainDbAddBlocks(chain, track, conn); return chain; } void linkToOtherBrowserExtra(char *otherDb, char *chrom, int start, int end, char *extra) /* Make anchor tag to open another browser window. */ { printf("<A TARGET=\"_blank\" HREF=\"%s?db=%s&%s&position=%s%%3A%d-%d\">", hgTracksName(), otherDb, extra, chrom, start+1, end); } void linkToOtherBrowserSearch(char *otherDb, char *tag) /* Make anchor tag to open another browser window. */ { printf("<A TARGET=\"_blank\" HREF=\"%s?db=%s&ct=&position=%s\">", hgTracksName(), otherDb, tag); } void linkToOtherBrowser(char *otherDb, char *chrom, int start, int end) /* Make anchor tag to open another browser window. */ { printf("<A TARGET=\"_blank\" HREF=\"%s?db=%s&ct=&position=%s%%3A%d-%d\">", hgTracksName(), otherDb, chrom, start+1, end); } void linkToOtherBrowserTitle(char *otherDb, char *chrom, int start, int end, char *title) /* Make anchor tag to open another browser window. */ { printf("<A TARGET=\"_blank\" TITLE=\"%s\" HREF=\"%s?db=%s&ct=&position=%s%%3A%d-%d\">", title, hgTracksName(), otherDb, chrom, start+1, end); } void chainToOtherBrowser(struct chain *chain, char *otherDb, char *otherOrg) /* Put up link that lets us use chain to browser on * corresponding window of other species. */ { struct chain *subChain = NULL, *toFree = NULL; int qs,qe; chainSubsetOnT(chain, winStart, winEnd, &subChain, &toFree); if (subChain != NULL && otherOrg != NULL) { qChainRangePlusStrand(subChain, &qs, &qe); linkToOtherBrowser(otherDb, subChain->qName, qs-1, qe); printf("Open %s browser</A> at position corresponding to the part of chain that is in this window.<BR>\n", otherOrg); } chainFree(&toFree); } void genericChainClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb) /* Handle click in chain track, at least the basics. */ { char *thisOrg = hOrganism(database); char *otherOrg = NULL; struct chain *chain = NULL, *subChain = NULL, *toFree = NULL; int chainWinSize; double subSetScore = 0.0; int qs, qe; boolean nullSubset = FALSE; if (! sameWord(otherDb, "seq")) { otherOrg = hOrganism(otherDb); } if (otherOrg == NULL) { /* use first word of chain label (count on org name as first word) */ otherOrg = firstWordInLine(cloneString(tdb->shortLabel)); } if (startsWith("big", tdb->type)) { char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); char *linkFileName = trackDbSetting(tdb, "linkDataUrl"); chain = chainLoadIdRangeHub(fileName, linkFileName, seqName, winStart, winEnd, atoi(item)); } else { chain = chainLoadIdRange(database, tdb->table, seqName, winStart, winEnd, atoi(item)); } chainSubsetOnT(chain, winStart, winEnd, &subChain, &toFree); if (subChain == NULL) nullSubset = TRUE; else if (hDbIsActive(otherDb) && subChain != chain) { char *linearGap = trackDbSettingOrDefault(tdb, "chainLinearGap", "loose"); struct gapCalc *gapCalc = gapCalcFromFile(linearGap); struct axtScoreScheme *scoreScheme = axtScoreSchemeDefault(); int qStart = subChain->qStart; int qEnd = subChain->qEnd ; struct dnaSeq *tSeq = hDnaFromSeq(database, subChain->tName, subChain->tStart, subChain->tEnd, dnaLower); struct dnaSeq *qSeq = NULL; char *matrix = trackDbSetting(tdb, "matrix"); if (matrix != NULL) { char *words[64]; int size = chopByWhite(matrix, words, 64) ; if (size == 2 && atoi(words[0]) == 16) { scoreScheme = axtScoreSchemeFromBlastzMatrix(words[1], 400, 30); } else { if (size != 2) errAbort("error parsing matrix entry in trackDb, expecting 2 word got %d ", size); else errAbort("error parsing matrix entry in trackDb, size 16 matrix, got %d ", atoi(words[0])); } } if (subChain->qStrand == '-') reverseIntRange(&qStart, &qEnd, subChain->qSize); qSeq = hChromSeq(otherDb, subChain->qName, qStart, qEnd); if (subChain->qStrand == '-') reverseComplement(qSeq->dna, qSeq->size); subChain->score = chainCalcScoreSubChain(subChain, scoreScheme, gapCalc, qSeq, tSeq); subSetScore = subChain->score; } chainFree(&toFree); printf("<B>%s position:</B> <A HREF=\"%s?%s&db=%s&position=%s:%d-%d\">%s:%d-%d</A>" " size: %d <BR>\n", thisOrg, hgTracksName(), cartSidUrlString(cart), database, chain->tName, chain->tStart+1, chain->tEnd, chain->tName, chain->tStart+1, chain->tEnd, chain->tEnd-chain->tStart); printf("<B>Strand:</B> %c<BR>\n", chain->qStrand); qChainRangePlusStrand(chain, &qs, &qe); if (sameWord(otherDb, "seq")) { printf("<B>%s position:</B> %s:%d-%d size: %d<BR>\n", otherOrg, chain->qName, qs, qe, chain->qEnd - chain->qStart); } else { /* prints link to other db browser only if db exists and is active */ /* else just print position with no link for the other db */ printf("<B>%s position: </B>", otherOrg); if (hDbIsActive(otherDb)) printf(" <A target=\"_blank\" href=\"%s?db=%s&position=%s%%3A%d-%d\">", hgTracksName(), otherDb, chain->qName, qs, qe); printf("%s:%d-%d", chain->qName, qs, qe); if (hDbIsActive(otherDb)) printf("</A>"); printf(" size: %d<BR>\n", chain->qEnd - chain->qStart); } printf("<B>Chain ID:</B> %s<BR>\n", item); printf("<B>Score:</B> %1.0f\n", chain->score); if (nullSubset) printf("<B>Score within browser window:</B> N/A (no aligned bases)<BR>\n"); else if (hDbIsActive(otherDb) && subChain != chain) printf("<B> Approximate Score within browser window:</B> %1.0f<BR>\n", subSetScore); else printf("<BR>\n"); boolean normScoreAvailable = chainDbNormScoreAvailable(tdb); if (normScoreAvailable) { char tableName[HDB_MAX_TABLE_STRING]; if (!hFindSplitTable(database, chain->tName, tdb->table, tableName, sizeof tableName, NULL)) errAbort("genericChainClick track %s not found", tdb->table); char query[256]; struct sqlResult *sr; char **row; sqlSafef(query, ArraySize(query), "select normScore from %s where id = '%s'", tableName, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { double normScore = atof(row[0]); int basesAligned = chain->score / normScore; printf("<B>Normalized Score:</B> %1.0f (aligned bases: %d)", normScore, basesAligned); } sqlFreeResult(&sr); printf("<BR>\n"); } printf("<BR>Fields above refer to entire chain or gap, not just the part inside the window.<BR>\n"); printf("<BR>\n"); chainWinSize = min(winEnd-winStart, chain->tEnd - chain->tStart); /* Show alignment if the database exists and */ /* if there is a chromInfo table for that database and the sequence */ /* file exists. This means that alignments can be shown on the archive */ /* server (or in other cases) if there is a database with a chromInfo table, */ /* the sequences are available and there is an entry added to dbDb for */ /* the otherDb. */ if (!startsWith("big", tdb->type) && sqlDatabaseExists(otherDb) && chromSeqFileExists(otherDb, chain->qName)) { if (chainWinSize < 1000000) { printf("View "); hgcAnchorSomewhere("htcChainAli", item, tdb->track, chain->tName); printf("DNA sequence alignment</A> details of parts of chain within browser " "window.<BR>\n"); } else { printf("Zoom so that browser window covers 1,000,000 bases or less " "and return here to see alignment details.<BR>\n"); } if (!sameWord(otherDb, "seq") && (hDbIsActive(otherDb))) { chainToOtherBrowser(chain, otherDb, otherOrg); } } /* if (!sameWord(otherDb, "seq") && (hDbIsActive(otherDb))) { chainToOtherBrowser(chain, otherDb, otherOrg); } */ chainFree(&chain); } char *trackTypeInfo(char *track) /* Return type info on track. You can freeMem result when done. */ { struct slName *trackDbs = hTrackDbList(), *oneTrackDb; struct sqlConnection *conn = hAllocConn(database); char buf[512]; char query[256]; for (oneTrackDb = trackDbs; oneTrackDb != NULL; oneTrackDb = oneTrackDb->next) { if (sqlTableExists(conn, oneTrackDb->name)) { sqlSafef(query, sizeof(query), "select type from %s where tableName = '%s'", oneTrackDb->name, track); if (sqlQuickQuery(conn, query, buf, sizeof(buf)) != NULL) break; } } if (oneTrackDb == NULL) errAbort("%s isn't in the trackDb from the hg.conf", track); slNameFreeList(&trackDbs); hFreeConn(&conn); return cloneString(buf); } void findNib(char *db, char *chrom, char nibFile[512]) /* Find nib file corresponding to chromosome in given database. */ { struct sqlConnection *conn = sqlConnect(db); char query[256]; sqlSafef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom); if (sqlQuickQuery(conn, query, nibFile, 512) == NULL) errAbort("Sequence %s isn't in database %s", chrom, db); sqlDisconnect(&conn); } struct dnaSeq *loadGenomePart(char *db, char *chrom, int start, int end) /* Load genomic dna from given database and position. */ { char nibFile[512]; findNib(db, chrom, nibFile); return hFetchSeq(nibFile, chrom, start, end); } void printLabeledNumber(char *org, char *label, long long number) /* Print label: in bold face, and number with commas. */ { char *space = " "; if (org == NULL) org = space = ""; printf("<B>%s%s%s:</B> ", org, space, label); printLongWithCommas(stdout, number); printf("<BR>\n"); } void printLabeledPercent(char *org, char *label, long p, long q) /* Print label: in bold, then p, and then 100 * p/q */ { char *space = " "; if (org == NULL) org = space = ""; printf("<B>%s%s%s:</B> ", org, space, label); printLongWithCommas(stdout, p); if (q != 0) printf(" (%3.1f%%)", 100.0 * p / q); printf("<BR>\n"); } void genericNetClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb, char *chainTrack) /* Generic click handler for net tracks. */ { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; char query[256]; struct sqlResult *sr; char **row; struct netAlign *net; char *org = hOrganism(database); char *otherOrg = hOrganism(otherDb); char *otherOrgBrowser = otherOrg; int tSize, qSize; int netWinSize; struct chain *chain; if (otherOrg == NULL) { /* use first word in short track label */ otherOrg = firstWordInLine(cloneString(tdb->shortLabel)); } if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("genericNetClick track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where tName = '%s' and tStart <= %d and tEnd > %d " "and level = %s", table, seqName, start, start, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s:%d in %s", seqName, start, table); net = netAlignLoad(row+hasBin); sqlFreeResult(&sr); tSize = net->tEnd - net->tStart; qSize = net->qEnd - net->qStart; if (net->chainId != 0) { netWinSize = min(winEnd-winStart, net->tEnd - net->tStart); printf("<BR>\n"); /* Show alignment if the database exists and */ /* if there is a chromInfo table for that database and the sequence */ /* file exists. This means that alignments can be shown on the archive */ /* server (or in other cases) if there is a database with a chromInfo */ /* table, the sequences are available and there is an entry added to */ /* dbDb for the otherDb. */ if (chromSeqFileExists(otherDb, net->qName)) { if (netWinSize < 1000000) { int ns = max(winStart, net->tStart); int ne = min(winEnd, net->tEnd); if (ns < ne) { char id[20]; snprintf(id, sizeof(id), "%d", net->chainId); hgcAnchorWindow("htcChainAli", id, ns, ne, chainTrack, seqName); printf("View alignment details of parts of net within browser window</A>.<BR>\n"); } else { printf("Odd, net not in window<BR>\n"); } } else { printf("To see alignment details zoom so that the browser window covers 1,000,000 bases or less.<BR>\n"); } } chain = chainDbLoad(conn, database, chainTrack, seqName, net->chainId); if (chain != NULL) { /* print link to browser for otherDb only if otherDb is active */ if (hDbIsActive(otherDb)) chainToOtherBrowser(chain, otherDb, otherOrgBrowser); chainFree(&chain); } htmlHorizontalLine(); } printf("<B>Type:</B> %s<BR>\n", net->type); printf("<B>Level:</B> %d<BR>\n", (net->level+1)/2); printf("<B>%s position:</B> %s:%d-%d<BR>\n", org, net->tName, net->tStart+1, net->tEnd); printf("<B>%s position:</B> %s:%d-%d<BR>\n", otherOrg, net->qName, net->qStart+1, net->qEnd); printf("<B>Strand:</B> %c<BR>\n", net->strand[0]); printLabeledNumber(NULL, "Score", net->score); if (net->chainId) { printf("<B>Chain ID:</B> %u<BR>\n", net->chainId); printLabeledNumber(NULL, "Bases aligning", net->ali); if (net->qOver >= 0) printLabeledNumber(otherOrg, "parent overlap", net->qOver); if (net->qFar >= 0) printLabeledNumber(otherOrg, "parent distance", net->qFar); if (net->qDup >= 0) printLabeledNumber(otherOrg, "bases duplicated", net->qDup); } if (net->tN >= 0) printLabeledPercent(org, "N's", net->tN, tSize); if (net->qN >= 0) printLabeledPercent(otherOrg, "N's", net->qN, qSize); if (net->tTrf >= 0) printLabeledPercent(org, "tandem repeat (trf) bases", net->tTrf, tSize); if (net->qTrf >= 0) printLabeledPercent(otherOrg, "tandem repeat (trf) bases", net->qTrf, qSize); if (net->tR >= 0) printLabeledPercent(org, "RepeatMasker bases", net->tR, tSize); if (net->qR >= 0) printLabeledPercent(otherOrg, "RepeatMasker bases", net->qR, qSize); if (net->tOldR >= 0) printLabeledPercent(org, "old repeat bases", net->tOldR, tSize); if (net->qOldR >= 0) printLabeledPercent(otherOrg, "old repeat bases", net->qOldR, qSize); if (net->tNewR >= 0) printLabeledPercent(org, "new repeat bases", net->tOldR, tSize); if (net->qNewR >= 0) printLabeledPercent(otherOrg, "new repeat bases", net->qOldR, qSize); if (net->tEnd >= net->tStart) printLabeledNumber(org, "size", net->tEnd - net->tStart); if (net->qEnd >= net->qStart) printLabeledNumber(otherOrg, "size", net->qEnd - net->qStart); printf("<BR>Fields above refer to entire chain or gap, not just the part inside the window.<BR>\n"); netAlignFree(&net); } void tfbsConsSites(struct trackDb *tdb, char *item) /* detail page for tfbsConsSites track */ { boolean printedPlus = FALSE; boolean printedMinus = FALSE; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; char query[512]; struct sqlResult *sr; char **row; struct tfbsConsSites *tfbsConsSites; struct tfbsConsSites *tfbsConsSitesList = NULL; struct tfbsConsFactors *tfbsConsFactor; struct tfbsConsFactors *tfbsConsFactorList = NULL; boolean firstTime = TRUE; char *mappedId = NULL; genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("tfbsConsSites track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbsConsSites = tfbsConsSitesLoad(row+hasBin); slAddHead(&tfbsConsSitesList, tfbsConsSites); } sqlFreeResult(&sr); slReverse(&tfbsConsSitesList); if (!hFindSplitTable(database, seqName, "tfbsConsFactors", table, sizeof table, &hasBin)) errAbort("tfbsConsSites table tfbsConsFactors not found"); sqlSafef(query, sizeof query, "select * from %s where name = '%s' ", table, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbsConsFactor = tfbsConsFactorsLoad(row+hasBin); slAddHead(&tfbsConsFactorList, tfbsConsFactor); } sqlFreeResult(&sr); slReverse(&tfbsConsFactorList); if (tfbsConsFactorList) mappedId = cloneString(tfbsConsFactorList->ac); printf("<B style='font-size:large;'>Transcription Factor Binding Site information:</B><BR><BR><BR>"); for(tfbsConsSites=tfbsConsSitesList ; tfbsConsSites != NULL ; tfbsConsSites = tfbsConsSites->next) { /* print each strand only once */ if ((printedMinus && (tfbsConsSites->strand[0] == '-')) || (printedPlus && (tfbsConsSites->strand[0] == '+'))) continue; if (!firstTime) htmlHorizontalLine(); else firstTime = FALSE; printf("<B>Item:</B> %s<BR>\n", tfbsConsSites->name); if (mappedId != NULL) printCustomUrl(tdb, mappedId, FALSE); printf("<B>Score:</B> %d<BR>\n", tfbsConsSites->score ); printf("<B>zScore:</B> %.2f<BR>\n", tfbsConsSites->zScore ); printf("<B>Strand:</B> %s<BR>\n", tfbsConsSites->strand); printPos(tfbsConsSites->chrom, tfbsConsSites->chromStart, tfbsConsSites->chromEnd, NULL, TRUE, tfbsConsSites->name); printedPlus = printedPlus || (tfbsConsSites->strand[0] == '+'); printedMinus = printedMinus || (tfbsConsSites->strand[0] == '-'); } if (tfbsConsFactorList) { htmlHorizontalLine(); printf("<B style='font-size:large;'>Transcription Factors known to bind to this site:</B><BR><BR>"); for(tfbsConsFactor =tfbsConsFactorList ; tfbsConsFactor != NULL ; tfbsConsFactor = tfbsConsFactor ->next) { if (!sameString(tfbsConsFactor->species, "N")) { printf("<BR><B>Factor:</B> %s<BR>\n", tfbsConsFactor->factor); printf("<B>Species:</B> %s<BR>\n", tfbsConsFactor->species); printf("<B>SwissProt ID:</B> %s<BR>\n", sameString(tfbsConsFactor->id, "N")? "unknown": tfbsConsFactor->id); } } } printTrackHtml(tdb); hFreeConn(&conn); } void tfbsCons(struct trackDb *tdb, char *item) /* detail page for tfbsCons track */ { boolean printFactors = FALSE; boolean printedPlus = FALSE; boolean printedMinus = FALSE; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; char query[512]; struct sqlResult *sr; char **row; struct tfbsCons *tfbs; struct tfbsCons *tfbsConsList = NULL; struct tfbsConsMap tfbsConsMap; boolean firstTime = TRUE; char *mappedId = NULL; genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("tfbsCons track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbs = tfbsConsLoad(row+hasBin); slAddHead(&tfbsConsList, tfbs); } sqlFreeResult(&sr); slReverse(&tfbsConsList); if (hTableExists(database, "tfbsConsMap")) { sqlSafef(query, sizeof query, "select * from tfbsConsMap where id = '%s'", tfbsConsList->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { tfbsConsMapStaticLoad(row, &tfbsConsMap); mappedId = cloneString(tfbsConsMap.ac); } } sqlFreeResult(&sr); printf("<B style='font-size:large;'>Transcription Factor Binding Site information:</B><BR><BR><BR>"); for(tfbs=tfbsConsList ; tfbs != NULL ; tfbs = tfbs->next) { if (!sameString(tfbs->species, "N")) printFactors = TRUE; /* print each strand only once */ if ((printedMinus && (tfbs->strand[0] == '-')) || (printedPlus && (tfbs->strand[0] == '+'))) continue; if (!firstTime) htmlHorizontalLine(); else firstTime = FALSE; printf("<B>Item:</B> %s<BR>\n", tfbs->name); if (mappedId != NULL) printCustomUrl(tdb, mappedId, FALSE); printf("<B>Score:</B> %d<BR>\n", tfbs->score ); printf("<B>Strand:</B> %s<BR>\n", tfbs->strand); printPos(tfbsConsList->chrom, tfbs->chromStart, tfbs->chromEnd, NULL, TRUE, tfbs->name); printedPlus = printedPlus || (tfbs->strand[0] == '+'); printedMinus = printedMinus || (tfbs->strand[0] == '-'); } if (printFactors) { htmlHorizontalLine(); printf("<B style='font-size:large;'>Transcription Factors known to bind to this site:</B><BR><BR>"); for(tfbs=tfbsConsList ; tfbs != NULL ; tfbs = tfbs->next) { /* print only the positive strand when factors are on both strands */ if ((tfbs->strand[0] == '-') && printedPlus) continue; if (!sameString(tfbs->species, "N")) { printf("<BR><B>Factor:</B> %s<BR>\n", tfbs->factor); printf("<B>Species:</B> %s<BR>\n", tfbs->species); printf("<B>SwissProt ID:</B> %s<BR>\n", sameString(tfbs->id, "N")? "unknown": tfbs->id); } } } printTrackHtml(tdb); hFreeConn(&conn); } void firstEF(struct trackDb *tdb, char *item) { int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; /* itemForUrl = item; */ genericHeader(tdb, item); printCustomUrl(tdb, item, FALSE); /* printCustomUrl(tdb, itemForUrl, item == itemForUrl); */ if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("firstEF track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 6); printf("<B>Item:</B> %s<BR>\n", bed->name); printf("<B>Probability:</B> %g<BR>\n", bed->score / 1000.0); printf("<B>Strand:</B> %s<BR>\n", bed->strand); printPos(bed->chrom, bed->chromStart, bed->chromEnd, NULL, TRUE, bed->name); } printTrackHtml(tdb); hFreeConn(&conn); } void doBed5FloatScore(struct trackDb *tdb, char *item) /* Handle click in BED 5+ track: BED 5 with 0-1000 score (for useScore * shading in hgTracks) plus real score for display in details page. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed5FloatScore *b5; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; int start = cartInt(cart, "o"); int bedSize = 5; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("doBed5FloatScore track %s not found", tdb->table); sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); hAddBinToQuery(winStart, winEnd, query); sqlDyStringPrintf(query, "name = '%s' and chromStart = %d", item, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); b5 = bed5FloatScoreLoad(row+hasBin); bedPrintPos((struct bed *)b5, 4, tdb); printf("<B>Score:</B> %f<BR>\n", b5->floatScore); if (sameString(tdb->type, "bed5FloatScoreWithFdr")) { if (row[7] != NULL) printf("<B>False Discovery Rate (FDR):</B> %s%%<BR>\n", row[7]); } } getBedTopScorers(conn, tdb, table, item, start, bedSize); sqlFreeResult(&sr); hFreeConn(&conn); /* printTrackHtml is done in genericClickHandlerPlus. */ } void doBed6FloatScore(struct trackDb *tdb, char *item) /* Handle click in BED 4+ track that's like BED 6 but with floating pt score */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed6FloatScore *b6 = NULL; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; int start = cartInt(cart, "o"); genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("doBed6FloatScore track %s not found", tdb->table); sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); hAddBinToQuery(winStart, winEnd, query); sqlDyStringPrintf(query, "name = '%s' and chromStart = %d", item, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); b6 = bed6FloatScoreLoad(row+hasBin); bedPrintPos((struct bed *)b6, 4, tdb); printf("<B>Score:</B> %f<BR>\n", b6->score); printf("<B>Strand:</B> %s<BR>\n", b6->strand); } sqlFreeResult(&sr); // Support for motif display if configured in trackDb // TODO - share code with factorSource char *motifPwmTable = trackDbSetting(tdb, "motifPwmTable"); struct dnaMotif *motif = NULL; if (motifPwmTable != NULL && sqlTableExists(conn, motifPwmTable)) { motif = loadDnaMotif(b6->name, motifPwmTable); if (motif == NULL) return; struct dnaSeq *seq = hDnaFromSeq(database, b6->chrom, b6->chromStart, b6->chromEnd, dnaLower); motifLogoAndMatrix(&seq, 1, motif); } hFreeConn(&conn); /* printTrackHtml is done in genericClickHandlerPlus. */ } void doColoredExon(struct trackDb *tdb, char *item) /* Print information for coloredExon type tracks. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select chrom,chromStart,chromEnd,name,score,strand from %s where name='%s'", tdb->table, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct bed *itemBed = bedLoad6(row); bedPrintPos(itemBed, 6, tdb); bedFree(&itemBed); } else { hPrintf("Could not find info for %s<BR>\n", item); } sqlFreeResult(&sr); printTrackHtml(tdb); hFreeConn(&conn); } void doImageItemBed(struct trackDb *tdb, char *item) /* Print bed plus an image */ { } void doChromGraph(struct trackDb *tdb) /* Print information for coloredExon type tracks. */ { genericHeader(tdb, NULL); printTrackHtml(tdb); } static void genericContainerClick(struct sqlConnection *conn, char *containerType, struct trackDb *tdb, char *item, char *itemForUrl) /* Print page for container of some sort. */ { if (sameString(containerType, "multiWig")) { errAbort("It's suprising that multiWig container gets to hgc. It should go to hgTrackUi."); } else { errAbort("Unrecognized container type %s for %s", containerType, tdb->track); } } static void doLongTabix(struct trackDb *tdb, char *item) /* Handle a click on a long range interaction */ { char *bigDataUrl = hashFindVal(tdb->settingsHash, "bigDataUrl"); struct bedTabixFile *btf = bedTabixFileMayOpen(bigDataUrl, NULL, 0, 0); char *chromName = cartString(cart, "c"); struct bed *list = bedTabixReadBeds(btf, chromName, winStart, winEnd, bedLoad5); bedTabixFileClose(&btf); unsigned maxWidth; struct longRange *longRangeList = parseLongTabix(list, &maxWidth, 0); struct longRange *longRange, *ourLongRange = NULL; unsigned itemNum = sqlUnsigned(item); unsigned count = slCount(longRangeList); double *doubleArray; AllocArray(doubleArray, count); int ii = 0; for(longRange = longRangeList; longRange; longRange = longRange->next, ii++) { if (longRange->id == itemNum) { ourLongRange = longRange; } doubleArray[ii] = longRange->score; } if (ourLongRange == NULL) errAbort("cannot find long range item with id %d\n", itemNum); printf("Item you clicked on:<BR>\n"); printf(" <B>ID:</B> %u<BR>\n", ourLongRange->id); if (!ourLongRange->hasColor) // if there's color, then there's no score in this format printf("<B>Score:</B> %g<BR>\n", ourLongRange->score); unsigned padding = (ourLongRange->e - ourLongRange->s) / 10; int s = ourLongRange->s - padding; int e = ourLongRange->e + padding; if (s < 0 ) s = 0; int chromSize = hChromSize(database, seqName); if (e > chromSize) e = chromSize; char sStartPosBuf[1024], sEndPosBuf[1024]; char eStartPosBuf[1024], eEndPosBuf[1024]; // FIXME: longRange should store region starts, not centers sprintLongWithCommas(sStartPosBuf, ourLongRange->s - ourLongRange->sw/2 + 1); sprintLongWithCommas(sEndPosBuf, ourLongRange->s + ourLongRange->sw/2 + 1); sprintLongWithCommas(eStartPosBuf, ourLongRange->e - ourLongRange->ew/2 + 1); sprintLongWithCommas(eEndPosBuf, ourLongRange->e + ourLongRange->ew/2 + 1); char sWidthBuf[1024], eWidthBuf[1024]; char regionWidthBuf[1024]; sprintLongWithCommas(sWidthBuf, ourLongRange->sw); sprintLongWithCommas(eWidthBuf, ourLongRange->ew); sprintLongWithCommas(regionWidthBuf, ourLongRange->ew + ourLongRange->e - ourLongRange->s); if (differentString(ourLongRange->sChrom, ourLongRange->eChrom)) { printf("<B>Current region: </B>"); printf("<A HREF=\"hgTracks?position=%s:%s-%s \" TARGET=_BLANK>%s:%s-%s (%s bp)</A><BR>\n", ourLongRange->sChrom, sStartPosBuf, sEndPosBuf, ourLongRange->sChrom, sStartPosBuf,sEndPosBuf, sWidthBuf); printf("<B>Paired region: </B>"); printf("<A HREF=\"hgTracks?position=%s:%s-%s \" TARGET=_BLANK>%s:%s-%s (%s bp)<BR></A><BR>\n", ourLongRange->eChrom, eStartPosBuf, eEndPosBuf, ourLongRange->eChrom, eStartPosBuf, eEndPosBuf, eWidthBuf); } else { printf("<B>Lower region: </B>"); printf("<A HREF=\"hgTracks?position=%s:%s-%s \" TARGET=_BLANK>%s:%s-%s (%s bp)</A><BR>\n", ourLongRange->sChrom, sStartPosBuf,sEndPosBuf, ourLongRange->sChrom, sStartPosBuf,sEndPosBuf, sWidthBuf); printf("<B>Upper region: </B>"); printf("<A HREF=\"hgTracks?position=%s:%s-%s \" TARGET=_BLANK>%s:%s-%s (%s bp)<BR></A><BR>\n", ourLongRange->eChrom, eStartPosBuf, eEndPosBuf, ourLongRange->eChrom, eStartPosBuf, eEndPosBuf, eWidthBuf); printf("<B>Interaction region: </B>"); printf("<A HREF=\"hgTracks?position=%s:%s-%s \" TARGET=_BLANK>%s:%s-%s (%s bp)<BR></A><BR>\n", ourLongRange->eChrom, sStartPosBuf, eEndPosBuf, ourLongRange->eChrom, sStartPosBuf, eEndPosBuf, regionWidthBuf); } if (ourLongRange->hasColor) return; struct aveStats *as = aveStatsCalc(doubleArray, count); printf("<BR>Statistics on the scores of all items in window (go to track controls to set minimum score to display):\n"); printf("<TABLE BORDER=1>\n"); printf("<TR><TD><B>Q1</B></TD><TD>%f</TD></TR>\n", as->q1); printf("<TR><TD><B>median</B></TD><TD>%f</TD></TR>\n", as->median); printf("<TR><TD><B>Q3</B></TD><TD>%f</TD></TR>\n", as->q3); printf("<TR><TD><B>average</B></TD><TD>%f</TD></TR>\n", as->average); printf("<TR><TD><B>min</B></TD><TD>%f</TD></TR>\n", as->minVal); printf("<TR><TD><B>max</B></TD><TD>%f</TD></TR>\n", as->maxVal); printf("<TR><TD><B>count</B></TD><TD>%d</TD></TR>\n", as->count); printf("<TR><TD><B>total</B></TD><TD>%f</TD></TR>\n", as->total); printf("<TR><TD><B>standard deviation</B></TD><TD>%f</TD></TR>\n", as->stdDev); printf("</TABLE>\n"); } void genericClickHandlerPlus( struct trackDb *tdb, char *item, char *itemForUrl, char *plus) /* Put up generic track info, with additional text appended after item. */ { char *dupe, *type, *words[16], *headerItem; int wordCount; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct sqlConnection *conn = NULL; char *imagePath = trackDbSetting(tdb, ITEM_IMAGE_PATH); char *container = trackDbSetting(tdb, "container"); if (!trackHubDatabase(database)) conn = hAllocConnTrack(database, tdb); if (itemForUrl == NULL) itemForUrl = item; dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); headerItem = cloneString(item); type = words[0]; /* Suppress printing item name in page header, as it is not informative for these types of * tracks... */ if (container == NULL && wordCount > 0) { if (sameString(type, "maf") || sameString(type, "wigMaf") || sameString(type, "bigMaf") || sameString(type, "netAlign") || sameString(type, "encodePeak")) headerItem = NULL; else if (( sameString(type, "narrowPeak") || sameString(type, "broadPeak") || sameString(type, "gappedPeak") ) && headerItem && sameString(headerItem, ".") ) headerItem = NULL; } /* Print header. */ genericHeader(tdb, headerItem); if (differentString(type, "bigInteract") && differentString(type, "interact")) { // skip generic URL code as these may have multiple items returned for a click itemForUrl = getIdInUrl(tdb, item); if (itemForUrl != NULL && trackDbSetting(tdb, "url")) { printCustomUrl(tdb, itemForUrl, item == itemForUrl); printIframe(tdb, itemForUrl); } } if (plus != NULL) { fputs(plus, stdout); } if (container != NULL) { genericContainerClick(conn, container, tdb, item, itemForUrl); } else if (wordCount > 0) { type = words[0]; if (sameString(type, "bed")) { int num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, item, start, num); } else if (sameString(type, "bigGenePred")) { int num = 12; genericBigBedClick(conn, tdb, item, start, end, num); } else if (sameString(type, "bigBed")) { int num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBigBedClick(conn, tdb, item, start, end, num); } else if (sameString(type, "sample")) { int num = 9; genericSampleClick(conn, tdb, item, start, num); } else if (sameString(type, "genePred")) { char *pepTable = NULL, *mrnaTable = NULL; if ((wordCount > 1) && !sameString(words[1], ".")) pepTable = words[1]; if ((wordCount > 2) && !sameString(words[2], ".")) mrnaTable = words[2]; genericGenePredClick(conn, tdb, item, start, pepTable, mrnaTable); } else if ( sameString(type, "bigPsl")) { genericBigPslClick(conn, tdb, item, start, end); } else if (sameString(type, "psl")) { char *subType = "."; if (wordCount > 1) subType = words[1]; genericPslClick(conn, tdb, item, start, subType); } else if (sameString(type, "netAlign")) { if (wordCount < 3) errAbort("Missing field in netAlign track type field"); genericNetClick(conn, tdb, item, start, words[1], words[2]); } else if (sameString(type, "chain") || sameString(type, "bigChain") ) { if (wordCount < 2) errAbort("Missing field in chain track type field"); genericChainClick(conn, tdb, item, start, words[1]); } else if (sameString(type, "maf")) { genericMafClick(conn, tdb, item, start); } else if (sameString(type, "wigMaf") || sameString(type, "bigMaf")) { genericMafClick(conn, tdb, item, start); } else if (startsWith("wigMafProt", type)) { genericMafClick(conn, tdb, item, start); } else if (sameString(type, "axt")) { genericAxtClick(conn, tdb, item, start, words[1]); } else if (sameString(type, "expRatio")) { doExpRatio(tdb, item, NULL); } else if (sameString(type, "coloredExon")) { doColoredExon(tdb, item); } else if (sameString(type, "encodePeak") || sameString(type, "narrowPeak") || sameString(type, "broadPeak") || sameString(type, "gappedPeak")) { doEncodePeak(tdb, NULL, item); } else if (sameString(type, "bigNarrowPeak")) { doBigEncodePeak(tdb, NULL, item); } else if (sameString(type, "encodeFiveC")) { doEncodeFiveC(conn, tdb); } else if (sameString(type, "peptideMapping")) { doPeptideMapping(conn, tdb, item); } else if (sameString(type, "chromGraph")) { doChromGraph(tdb); } else if (sameString(type, "wig")) { genericWiggleClick(conn, tdb, item, start); } else if (sameString(type, "bigWig")) { genericBigWigClick(conn, tdb, item, start); } else if (sameString(type, "factorSource")) { doFactorSource(conn, tdb, item, start, end); } else if (sameString(type, "bed5FloatScore") || sameString(type, "bed5FloatScoreWithFdr")) { doBed5FloatScore(tdb, item); } else if (sameString(type, "bed6FloatScore")) { doBed6FloatScore(tdb, item); } else if (sameString(type, "altGraphX")) { doAltGraphXDetails(tdb,item); } //add bedDetail here else if (startsWith("bedDetail", type)) { doBedDetail(tdb, NULL, item); } else if (sameString(type, "bigLolly") ) { int num = 12; genericBigBedClick(conn, tdb, item, start, end, num); } else if (sameString(type, "bigDbSnp") ) { doBigDbSnp(tdb, item); } else if (sameString(type, "interaction") ) { int num = 12; genericBedClick(conn, tdb, item, start, num); } else if (startsWith("gvf", type)) { doGvf(tdb, item); } else if (sameString(type, "bam")) doBamDetails(tdb, item); else if ( startsWith("longTabix", type)) doLongTabix(tdb, item); else if (sameWord("interact", type) || sameWord("bigInteract", type)) doInteractDetails(tdb, item); } if (imagePath) { char *bigImagePath = trackDbSettingClosestToHome(tdb, ITEM_BIG_IMAGE_PATH); char *bothWords[2]; int shouldBeTwo = chopLine(imagePath, bothWords); if (shouldBeTwo != 2) errAbort("itemImagePath setting for %s track incorrect. Needs to be \"itemImagePath <path> <suffix>\".", tdb->track); printf("<BR><IMG SRC=\"%s/%s.%s\"><BR><BR>\n", bothWords[0], item, bothWords[1]); shouldBeTwo = chopLine(bigImagePath, bothWords); if (shouldBeTwo != 2) errAbort("bigItemImagePath setting for %s track incorrect. Needs to be \"itemImagePath <path> <suffix>\".", tdb->track); printf("<A HREF=\"%s/%s.%s\">Download Original Image</A><BR>\n", bothWords[0], item, bothWords[1]); } if ((sameString(tdb->table,"altLocations") || sameString(tdb->table,"fixLocations")) && strchr(item,'_')) { // Truncate item (alt/fix sequence name) at colon if found: char itemCpy[strlen(item)+1]; safecpy(itemCpy, sizeof(itemCpy), item); char *p = strchr(itemCpy, ':'); if (p) *p = '\0'; char *hgsid = cartSessionId(cart); char *desc = sameString(tdb->table, "altLocations") ? "alternate haplotype" : "fix patch"; printf("<A HREF=\"hgTracks?hgsid=%s&virtModeType=singleAltHaplo&singleAltHaploId=%s\">" "Show this %s placed on its chromosome</A><BR>\n", hgsid, itemCpy, desc); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void genericClickHandler(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up generic track info */ { #ifdef OLD /* Called now by cartWebStart... */ jsIncludeFile("jquery.js", NULL); jsIncludeFile("utils.js",NULL); #endif /* OLD */ genericClickHandlerPlus(tdb, item, itemForUrl, NULL); } void savePosInTextBox(char *chrom, int start, int end) /* Save basic position/database info in text box and hidden var. Positions becomes chrom:start-end*/ { char position[128]; char *newPos; snprintf(position, 128, "%s:%d-%d", chrom, start, end); newPos = addCommasToPos(database, position); cgiMakeTextVar("getDnaPos", newPos, strlen(newPos) + 2); cgiContinueHiddenVar("db"); } char *hgTablesUrl(boolean usePos, char *track) /* Make up URL for table browser. */ { struct dyString *url = dyStringNew(0); dyStringAppend(url, "../cgi-bin/hgTables?"); dyStringAppend(url, cartSidUrlString(cart)); dyStringPrintf(url, "&db=%s", database); if (usePos) { dyStringPrintf(url, "&position=%s:%d-%d", seqName, winStart+1, winEnd); dyStringAppend(url, "&hgta_regionType=range"); } if (track != NULL) { struct trackDb *tdb = hashFindVal(trackHash, track); if (tdb != NULL) { char *grp = tdb->grp; if (grp != NULL && grp[0] != 0) { dyStringPrintf(url, "&hgta_group=%s", grp); dyStringPrintf(url, "&hgta_track=%s", track); dyStringPrintf(url, "&hgta_table=%s", track); } } } return dyStringCannibalize(&url); } char *traceUrl(char *traceId) /* Make up URL for trace archive. */ { struct dyString *url = dyStringNew(0); dyStringAppend(url, "https://www.ncbi.nlm.nih.gov/Traces/trace.cgi?"); dyStringPrintf(url, "cmd=retrieve&size=1&val=%s&", traceId); dyStringAppend(url, "file=trace&dopt=trace"); return dyStringCannibalize(&url); } void doGetDna1() /* Do first get DNA dialog. */ { struct hTableInfo *hti = NULL; char *tbl = cgiUsualString("table", ""); if (dbIsFound && tbl[0] != 0) { char rootName[256]; char parsedChrom[32]; hParseTableName(database, tbl, rootName, parsedChrom); if (!trackHubDatabase(database)) hti = hFindTableInfo(database, seqName, rootName); } char *thisOrg = hOrganism(database); cartWebStart(cart, database, "Get DNA in Window (%s/%s)", database, thisOrg); printf("<H2>Get DNA for </H2>\n"); printf("<FORM ACTION=\"%s\">\n\n", hgcName()); cartSaveSession(cart); cgiMakeHiddenVar("g", "htcGetDna2"); cgiMakeHiddenVar("table", tbl); cgiContinueHiddenVar("i"); cgiContinueHiddenVar("o"); cgiContinueHiddenVar("t"); cgiContinueHiddenVar("l"); cgiContinueHiddenVar("r"); puts("Position "); savePosInTextBox(seqName, winStart+1, winEnd); if (tbl[0] == 0) { puts("<P>" "Note: This page retrieves genomic DNA for a single region. " "If you would prefer to get DNA for many items in a particular track, " "or get DNA with formatting options based on gene structure (introns, exons, UTRs, etc.), try using the "); printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(TRUE, NULL)); puts("Table Browser</A> with the \"sequence\" output format. You can also use the "); printf("<A HREF=\"../goldenPath/help/api.html\" TARGET=_blank>"); puts("REST API</A> with the <b>/getData/sequence</b> endpoint function " "to extract sequence data with coordinates."); } else { puts("<P>" "Note: if you would prefer to get DNA for more than one feature of " "this track at a time, try the "); printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(FALSE, tbl)); puts("Table Browser</A> using the output format sequence."); } hgSeqOptionsHtiCart(hti,cart); puts("<P>"); cgiMakeButton("submit", "get DNA"); if (dbIsFound) cgiMakeButton("submit", EXTENDED_DNA_BUTTON); puts("</FORM><P>"); if (dbIsFound) puts("Note: The \"Mask repeats\" option applies only to \"get DNA\", not to \"extended case/color options\". <P>"); } boolean dnaIgnoreTrack(char *track) /* Return TRUE if this is one of the tracks too boring * to put DNA on. */ { return (sameString("cytoBand", track) || sameString("gcPercent", track) || sameString("gold", track) || sameString("gap", track) || startsWith("mouseSyn", track)); } struct customTrack *getCtList() /* initialize theCtList if necessary and return it */ { if (theCtList == NULL) theCtList = customTracksParseCart(database, cart, NULL, NULL); return(theCtList); } struct trackDb *tdbForCustomTracks() /* Load custom tracks (if any) and translate to list of trackDbs */ { struct customTrack *ctList = getCtList(); struct customTrack *ct; struct trackDb *tdbList = NULL, *tdb; for (ct=ctList; ct != NULL; ct=ct->next) { AllocVar(tdb); tdb->track = ct->tdb->track; tdb->table = ct->tdb->table; tdb->shortLabel = ct->tdb->shortLabel; tdb->type = ct->tdb->type; tdb->longLabel = ct->tdb->longLabel; tdb->visibility = ct->tdb->visibility; tdb->priority = ct->tdb->priority; tdb->colorR = ct->tdb->colorR; tdb->colorG = ct->tdb->colorG; tdb->colorB = ct->tdb->colorB; tdb->altColorR = ct->tdb->altColorR; tdb->altColorG = ct->tdb->altColorG; tdb->altColorB = ct->tdb->altColorB; tdb->useScore = ct->tdb->useScore; tdb->private = ct->tdb->private; tdb->url = ct->tdb->url; tdb->grp = ct->tdb->grp; tdb->canPack = ct->tdb->canPack; trackDbPolish(tdb); slAddHead(&tdbList, tdb); } slReverse(&tdbList); return(tdbList); } struct customTrack *lookupCt(char *name) /* Return custom track for name, or NULL. */ { struct customTrack *ct; for (ct=getCtList(); ct != NULL; ct=ct->next) if (sameString(name, ct->tdb->track)) return(ct); return(NULL); } void parseSs(char *ss, char **retPslName, char **retFaName, char **retQName) /* Parse space separated 'ss' item. */ { static char buf[512*2]; int wordCount; char *words[4]; strcpy(buf, ss); wordCount = chopLine(buf, words); if (wordCount < 1) errAbort("Empty user cart variable ss."); *retPslName = words[0]; if (retFaName != NULL) { if (wordCount < 2) errAbort("Expecting psl filename and fa filename in cart variable ss, but only got one word: %s", ss); *retFaName = words[1]; } if (retQName != NULL) { if (wordCount < 3) errAbort("Expecting psl filename, fa filename and query name in cart variable ss, but got this: %s", ss); *retQName = words[2]; } } boolean ssFilesExist(char *ss) /* Return TRUE if both files in ss exist. -- Copied from hgTracks! */ { char *faFileName, *pslFileName; parseSs(ss, &pslFileName, &faFileName, NULL); return fileExists(pslFileName) && fileExists(faFileName); } struct trackDb *tdbForUserPsl() /* Load up user's BLAT results into trackDb. */ { char *ss = cartOptionalString(cart, "ss"); if ((ss != NULL) && !ssFilesExist(ss)) { ss = NULL; cartRemove(cart, "ss"); } if (ss == NULL) return(NULL); else { struct trackDb *tdb; AllocVar(tdb); tdb->track = cloneString(USER_PSL_TRACK_NAME); tdb->table = cloneString(USER_PSL_TRACK_NAME); tdb->shortLabel = cloneString(USER_PSL_TRACK_LABEL); tdb->type = cloneString("psl"); tdb->longLabel = cloneString(USER_PSL_TRACK_LONGLABEL); tdb->visibility = tvFull; tdb->priority = 11.0; trackDbPolish(tdb); return(tdb); } } struct trackDb *rFindUnderstandableTrack(char *db, struct trackDb *tdb) // If any leaf is usable in getting DNA then that leaf's tdb is returned. { if (tdb->subtracks != NULL) return rFindUnderstandableTrack(db,tdb->subtracks); if (fbUnderstandTrack(db, tdb->table) && !dnaIgnoreTrack(tdb->table)) return tdb; else return NULL; } boolean forestHasUnderstandableTrack(char *db, struct trackDb *tdb) // TRUE if any leaf is usable in getting DNA. { return (rFindUnderstandableTrack(db, tdb) != NULL); } void doGetDnaExtended1() /* Do extended case/color get DNA options. */ { struct trackDb *tdbList = hTrackDb(database), *tdb; struct trackDb *ctdbList = tdbForCustomTracks(); struct trackDb *utdbList = tdbForUserPsl(); boolean revComp = cartUsualBoolean(cart, "hgSeq.revComp", FALSE); boolean maskRep = cartUsualBoolean(cart, "hgSeq.maskRepeats", FALSE); int padding5 = cartUsualInt(cart, "hgSeq.padding5", 0); int padding3 = cartUsualInt(cart, "hgSeq.padding3", 0); int lineWidth = cartUsualInt(cart, "lineWidth", 60); char *casing = cartUsualString(cart, "hgSeq.casing", ""); char *repMasking = cartUsualString(cart, "hgSeq.repMasking", ""); boolean caseUpper= FALSE; char *pos = NULL; ctdbList = slCat(ctdbList, tdbList); tdbList = slCat(utdbList, ctdbList); cartWebStart(cart, database, "Extended DNA Case/Color"); if (NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos")))) hgParseChromRange(database, pos, &seqName, &winStart, &winEnd); if (winEnd - winStart > 5000000) { printf("Please zoom in to 5 million bases or less to color the DNA"); return; } printf("<H1>Extended DNA Case/Color Options</H1>\n"); puts( "Use this page to highlight features in genomic DNA text. " "DNA covered by a particular track can be highlighted by " "case, underline, bold, italic, or color. See below for " "details about color, and for examples. <B>Tracks in " ""hide" display mode are not shown in the grid below.</B> <P>"); if (cgiBooleanDefined("hgSeq.maskRepeats")) cartSetBoolean(cart, "hgSeq.maskRepeats", maskRep); if (*repMasking != 0) cartSetString(cart, "hgSeq.repMasking", repMasking); if (maskRep) { struct trackDb *rtdb; char *visString = cartOptionalString(cart, "rmsk"); for (rtdb = tdbList; rtdb != NULL; rtdb=rtdb->next) { if (startsWith(rtdb->table, "rmsk")) break; } printf("<P> <B>Note:</B> repeat masking style from previous page will <B>not</B> apply to this page.\n"); if ((rtdb != NULL) && ((visString == NULL) || !sameString(visString, "hide"))) printf("Use the case/color options for the RepeatMasker track below. <P>\n"); else printf("Unhide the RepeatMasker track in the genome browser, then return to this page and use the case/color options for the RepeatMasker track below. <P>\n"); } cartSetInt(cart, "padding5", padding5); cartSetInt(cart, "padding3", padding3); if (sameString(casing, "upper")) caseUpper = TRUE; if (*casing != 0) cartSetString(cart, "hgSeq.casing", casing); printf("<FORM ACTION=\"%s\" METHOD=\"POST\">\n\n", hgcName()); cartSaveSession(cart); cgiMakeHiddenVar("g", "htcGetDna3"); if (NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos")))) { hgParseChromRange(database, pos, &seqName, &winStart, &winEnd); } puts("Position "); savePosInTextBox(seqName, winStart+1 - (revComp ? padding3 : padding5), winEnd + (revComp ? padding5 : padding3)); printf(" Reverse complement "); cgiMakeCheckBox("hgSeq.revComp", revComp); printf("<BR>\n"); printf("Letters per line "); cgiMakeIntVar("lineWidth", lineWidth, 3); printf(" Default case: "); cgiMakeRadioButton("hgSeq.casing", "upper", caseUpper); printf(" Upper "); cgiMakeRadioButton("hgSeq.casing", "lower", !caseUpper); printf(" Lower "); cgiMakeButton("Submit", "submit"); printf("<BR>\n"); printf("<TABLE BORDER=1>\n"); printf("<TR><TD>Track<BR>Name</TD><TD>Toggle<BR>Case</TD><TD>Under-<BR>line</TD><TD>Bold</TD><TD>Italic</TD><TD>Red</TD><TD>Green</TD><TD>Blue</TD></TR>\n"); for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { char *table = tdb->table; char *track = tdb->track; if ( sameString(USER_PSL_TRACK_NAME, table) || lookupCt(track) != NULL || ( tdbVisLimitedByAncestors(cart,tdb,TRUE,TRUE) != tvHide && forestHasUnderstandableTrack(database, tdb) ) ) { char *visString = cartUsualString(cart, track, hStringFromTv(tdb->visibility)); if (differentString(visString, "hide") && tdb->parent) { char *parentVisString = cartUsualString(cart, tdb->parentName, hStringFromTv(tdb->parent->visibility)); if (sameString("hide", parentVisString)) visString = "hide"; } char buf[128]; if (sameString(visString, "hide")) { char varName[256]; safef(varName, sizeof varName, "%s_case", track); cartSetBoolean(cart, varName, FALSE); safef(varName, sizeof varName, "%s_u", track); cartSetBoolean(cart, varName, FALSE); safef(varName, sizeof varName, "%s_b", track); cartSetBoolean(cart, varName, FALSE); safef(varName, sizeof varName, "%s_i", track); cartSetBoolean(cart, varName, FALSE); safef(varName, sizeof varName, "%s_red", track); cartSetInt(cart, varName, 0); safef(varName, sizeof varName, "%s_green", track); cartSetInt(cart, varName, 0); safef(varName, sizeof varName, "%s_blue", track); cartSetInt(cart, varName, 0); } else { printf("<TR>"); printf("<TD>%s</TD>", tdb->shortLabel); safef(buf, sizeof buf, "%s_case", tdb->track); printf("<TD>"); cgiMakeCheckBox(buf, cartUsualBoolean(cart, buf, FALSE)); printf("</TD>"); safef(buf, sizeof buf, "%s_u", tdb->track); printf("<TD>"); cgiMakeCheckBox(buf, cartUsualBoolean(cart, buf, FALSE)); printf("</TD>"); safef(buf, sizeof buf, "%s_b", tdb->track); printf("<TD>"); cgiMakeCheckBox(buf, cartUsualBoolean(cart, buf, FALSE)); printf("</TD>"); safef(buf, sizeof buf, "%s_i", tdb->track); printf("<TD>"); cgiMakeCheckBox(buf, cartUsualBoolean(cart, buf, FALSE)); printf("</TD>"); printf("<TD>"); safef(buf, sizeof buf, "%s_red", tdb->track); cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3); printf("</TD>"); printf("<TD>"); safef(buf, sizeof buf, "%s_green", tdb->track); cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3); printf("</TD>"); printf("<TD>"); safef(buf, sizeof buf, "%s_blue", tdb->track); cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3); printf("</TD>"); printf("</TR>\n"); } } } printf("</TABLE>\n"); printf("</FORM>\n"); printf("<H3>Coloring Information and Examples</H3>\n"); puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n"); puts("The examples below show a few ways to highlight individual tracks, " "and their interplay. It's good to keep it simple at first. It's easy " "to make pretty, but completely cryptic, displays with this feature."); puts( "<UL>" "<LI>To put exons from RefSeq Genes in upper case red text, check the " "appropriate box in the Toggle Case column and set the color to pure " "red, RGB (255,0,0). Upon submitting, any RefSeq Gene within the " "designated chromosomal interval will now appear in red capital letters.\n" "<LI>To see the overlap between RefSeq Genes and Genscan predictions try " "setting the RefSeq Genes to red (255,0,0) and Genscan to green (0,255,0). " "Places where the RefSeq Genes and Genscan overlap will be painted yellow " "(255,255,0).\n" "<LI>To get a level-of-coverage effect for tracks like Spliced Ests with " "multiple overlapping items, initially select a darker color such as deep " "green, RGB (0,64,0). Nucleotides covered by a single EST will appear dark " "green, while regions covered with more ESTs get progressively brighter — " "saturating at 4 ESTs." "<LI>Another track can be used to mask unwanted features. Setting the " "RepeatMasker track to RGB (255,255,255) will white-out Genscan predictions " "of LINEs but not mainstream host genes; masking with RefSeq Genes will show " "what is new in the gene prediction sector." "</UL>"); puts("<H3>Further Details and Ideas</H3>"); puts("<P>Copying and pasting the web page output to a text editor such as Word " "will retain upper case but lose colors and other formatting. That is still " "useful because other web tools such as " "<A HREF=\"https://www.ncbi.nlm.nih.gov/blast\" TARGET=_BLANK>NCBI Blast</A> " "can be set to ignore lower case. To fully capture formatting such as color " "and underlining, view the output as \"source\" in your web browser, or download " "it, or copy the output page into an html editor.</P>"); puts("<P>The default line width of 60 characters is standard, but if you have " "a reasonable sized monitor it's useful to set this higher - to 125 characters " "or more. You can see more DNA at once this way, and fewer line breaks help " "in finding DNA strings using the web browser search function.</P>"); puts("<P>Be careful about requesting complex formatting for a very large " "chromosomal region. After all the html tags are added to the output page, " "the file size may exceed size limits that your browser, clipboard, and " "other software can safely display. The tool will format 10 Mb and more, however.</P>"); trackDbFreeList(&tdbList); } void doGetBlastPep(char *readName, char *table) /* get predicted protein */ { int qStart; struct psl *psl; int start, end; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *tSeq; char query[256], **row; char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin; char *buffer, *str; int i, j; char *ptr; start = cartInt(cart, "o"); if (!hFindSplitTable(database, seqName, table, fullTable, sizeof fullTable, &hasBin)) errAbort("doGetBlastPep track %s not found", table); sqlSafef(query, sizeof query, "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", fullTable, readName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", readName, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); hFreeConn(&conn); printf("<PRE><TT>"); end = psl->tEnd; if (psl->strand[1] == '+') end = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1] *3; if ((ptr = strchr(readName, '.')) != NULL) *ptr++ = 0; printf(">%s-%s\n", readName,database); tSeq = hDnaFromSeq(database, psl->tName, start, end, dnaLower); if (psl->strand[1] == '-') { start = psl->tSize - end; reverseComplement(tSeq->dna, tSeq->size); } str = buffer = needMem(psl->qSize + 1); qStart = 0; for (i=0; i<psl->blockCount; ++i) { int ts = psl->tStarts[i] - start; int sz = psl->blockSizes[i]; for (;qStart < psl->qStarts[i]; qStart++) *str++ = 'X'; for (j=0; j<sz; ++j) { int codonStart = ts + 3*j; DNA *codon = &tSeq->dna[codonStart]; if ((*str = lookupCodon(codon)) == 0) *str = '*'; str++; qStart++; } } *str = 0; printLines(stdout, buffer, 50); printf("</TT></PRE>"); } void doGetDna2() /* Do second DNA dialog (or just fetch DNA) */ { char *tbl = cgiUsualString("table", ""); char *action = cgiUsualString("submit", ""); int itemCount; char *pos = NULL; char *chrom = NULL; int start = 0; int end = 0; if (sameString(action, EXTENDED_DNA_BUTTON)) { doGetDnaExtended1(); return; } // This output probably should be just text/plain but // trying to support the fancy warn handler box requires html. // But we want to keep it very simple and close to a plain text dump. cartHtmlStart("DNA"); puts("<PRE>"); if (tbl[0] == 0) { itemCount = 1; if ( NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos"))) && hgParseChromRange((dbIsFound ? database : NULL), pos, &chrom, &start, &end)) { hgSeqRange(database, chrom, start, end, '?', "dna"); } else { hgSeqRange(database, seqName, cartInt(cart, "l"), cartInt(cart, "r"), '?', "dna"); } } else { struct hTableInfo *hti = NULL; char rootName[256]; char parsedChrom[32]; /* use the values from the dnaPos dialog box */ if (!( NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos"))) && hgParseChromRange(database, pos, &chrom, &start, &end))) { /* if can't get DnaPos from dialog box, use "o" and "t" */ start = cartInt(cart, "o"); end = cartInt(cart, "t"); } /* Table might be a custom track if it's not in the database, * or bigBed if it is in the database but has only one column called 'fileName'; * in which case, just get DNA as if no table were given. */ hParseTableName(database, tbl, rootName, parsedChrom); if (!trackHubDatabase(database)) hti = hFindTableInfo(database, seqName, rootName); if (hti == NULL || hti->startField[0] == 0) { itemCount = 1; hgSeqRange(database, seqName, start, end, '?', tbl); } else { char *where = NULL; char *item = cgiUsualString("i", ""); char buf[256]; if ((hti->nameField[0] != 0) && (item[0] != 0)) { char *quotedItem = makeQuotedString(item, '\''); safef(buf, sizeof(buf), "%s = %s", hti->nameField, quotedItem); where = buf; freeMem(quotedItem); } itemCount = hgSeqItemsInRange(database, tbl, seqName, start, end, where); } } if (itemCount == 0) printf("\n# No results returned from query.\n\n"); puts("</PRE>"); } struct hTableInfo *ctToHti(struct customTrack *ct) /* Create an hTableInfo from a customTrack. */ { struct hTableInfo *hti; AllocVar(hti); hti->rootName = cloneString(ct->tdb->table); hti->isPos = TRUE; hti->isSplit = FALSE; hti->hasBin = FALSE; hti->type = cloneString(ct->tdb->type); int fieldCount = 3; if (sameWord(ct->dbTrackType, "bedDetail")) fieldCount = ct->fieldCount - 2; else if (sameWord(ct->dbTrackType, "pgSnp")) fieldCount = 4; else fieldCount = ct->fieldCount; if (fieldCount >= 3) { strncpy(hti->chromField, "chrom", 32); strncpy(hti->startField, "chromStart", 32); strncpy(hti->endField, "chromEnd", 32); } if (fieldCount >= 4) { strncpy(hti->nameField, "name", 32); } if (fieldCount >= 5) { strncpy(hti->scoreField, "score", 32); } if (fieldCount >= 6) { strncpy(hti->strandField, "strand", 32); } if (fieldCount >= 8) { strncpy(hti->cdsStartField, "thickStart", 32); strncpy(hti->cdsEndField, "thickEnd", 32); hti->hasCDS = TRUE; } if (fieldCount >= 12) { strncpy(hti->countField, "blockCount", 32); strncpy(hti->startsField, "chromStarts", 32); strncpy(hti->endsSizesField, "blockSizes", 32); hti->hasBlocks = TRUE; } return(hti); } struct hTableInfo *htiForUserPsl() /* Create an hTableInfo for user's BLAT results. */ { struct hTableInfo *hti; AllocVar(hti); hti->rootName = cloneString(USER_PSL_TRACK_NAME); hti->isPos = TRUE; hti->isSplit = FALSE; hti->hasBin = FALSE; hti->type = cloneString("psl"); strncpy(hti->chromField, "tName", 32); strncpy(hti->startField, "tStart", 32); strncpy(hti->endField, "tEnd", 32); strncpy(hti->nameField, "qName", 32); /* psl can be scored... but strictly speaking, does not have a score field! */ strncpy(hti->strandField, "strand", 32); hti->hasCDS = FALSE; strncpy(hti->countField, "blockCount", 32); strncpy(hti->startsField, "tStarts", 32); strncpy(hti->endsSizesField, "tSizes", 32); hti->hasBlocks = TRUE; return(hti); } struct bed *bedFromUserPsl() /* Load up user's BLAT results into bedList. */ { struct bed *bedList = NULL; char *ss = cartOptionalString(cart, "ss"); if ((ss != NULL) && ! ssFilesExist(ss)) { ss = NULL; cartRemove(cart, "ss"); } if (ss == NULL) return(NULL); else { struct lineFile *f; struct psl *psl; enum gfType qt, tt; char *faFileName, *pslFileName; int i; parseSs(ss, &pslFileName, &faFileName, NULL); pslxFileOpen(pslFileName, &qt, &tt, &f); while ((psl = pslNext(f)) != NULL) { struct bed *bed; AllocVar(bed); bed->chrom = cloneString(seqName); bed->chromStart = psl->tStart; bed->chromEnd = psl->tEnd; bed->name = cloneString(psl->qName); bed->score = pslScore(psl); if ((psl->strand[0] == '-' && psl->strand[1] == '+') || (psl->strand[0] == '+' && psl->strand[1] == '-')) strncpy(bed->strand, "-", 2); else strncpy(bed->strand, "+", 2); bed->thickStart = bed->chromStart; bed->thickEnd = bed->chromEnd; bed->blockCount = psl->blockCount; bed->chromStarts = needMem(bed->blockCount * sizeof(int)); bed->blockSizes = needMem(bed->blockCount * sizeof(int)); for (i=0; i < bed->blockCount; i++) { bed->chromStarts[i] = psl->tStarts[i]; bed->blockSizes[i] = psl->blockSizes[i]; } if (qt == gftProt) for (i=0; i < bed->blockCount; i++) { /* If query is protein, blockSizes are in aa units; fix 'em. */ bed->blockSizes[i] *= 3; } if (psl->strand[1] == '-') { /* psl: if target strand is '-', flip the coords. * (this is the target part of pslRc from src/lib/psl.c) */ for (i=0; i < bed->blockCount; ++i) { bed->chromStarts[i] = psl->tSize - (bed->chromStarts[i] + bed->blockSizes[i]); } reverseInts(bed->chromStarts, bed->blockCount); reverseInts(bed->blockSizes, bed->blockCount); assert(bed->chromStart == bed->chromStarts[0]); } /* translate absolute starts to relative starts (after handling * target-strand coord-flipping) */ for (i=0; i < bed->blockCount; i++) { bed->chromStarts[i] -= bed->chromStart; } slAddHead(&bedList, bed); pslFree(&psl); } lineFileClose(&f); slReverse(&bedList); return(bedList); } } void addColorToRange(int r, int g, int b, struct rgbColor *colors, int start, int end) /* Add rgb values to colors array from start to end. Don't let values * exceed 255 */ { struct rgbColor *c; int rr, gg, bb; int i; for (i=start; i<end; ++i) { c = colors+i; rr = c->r + r; if (rr > 255) rr = 255; c->r = rr; gg = c->g + g; if (gg > 255) gg = 255; c->g = gg; bb = c->b + b; if (bb > 255) bb = 255; c->b = bb; } } void getDnaHandleBits(char *track, char *type, Bits *bits, int winStart, int winEnd, boolean isRc, struct featureBits *fbList) /* See if track_type variable exists, and if so set corresponding bits. */ { char buf[256]; struct featureBits *fb; int s,e; int winSize = winEnd - winStart; safef(buf, sizeof buf, "%s_%s", track, type); if (cgiBoolean(buf)) { for (fb = fbList; fb != NULL; fb = fb->next) { s = fb->start - winStart; e = fb->end - winStart; if (isRc) reverseIntRange(&s, &e, winSize); bitSetRange(bits, s, e - s); } } } void doGetDna3() /* Fetch DNA in extended color format */ { struct dnaSeq *seq; struct cfm *cfm; int i; boolean isRc = cartUsualBoolean(cart, "hgSeq.revComp", FALSE); boolean defaultUpper = sameString(cartString(cart, "hgSeq.casing"), "upper"); int winSize; int lineWidth = cartInt(cart, "lineWidth"); struct rgbColor *colors; struct trackDb *tdbList = hTrackDb(database), *tdb; struct trackDb *ctdbList = tdbForCustomTracks(); struct trackDb *utdbList = tdbForUserPsl(); char *pos = NULL; Bits *uBits; /* Underline bits. */ Bits *iBits; /* Italic bits. */ Bits *bBits; /* Bold bits. */ if (NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos")))) hgParseChromRange(database, pos, &seqName, &winStart, &winEnd); winSize = winEnd - winStart; uBits = bitAlloc(winSize); /* Underline bits. */ iBits = bitAlloc(winSize); /* Italic bits. */ bBits = bitAlloc(winSize); /* Bold bits. */ ctdbList = slCat(ctdbList, tdbList); tdbList = slCat(utdbList, ctdbList); cartWebStart(cart, database, "Extended DNA Output"); printf("<PRE><TT>"); printf(">%s:%d-%d %s\n", seqName, winStart+1, winEnd, (isRc ? "(reverse complement)" : "")); seq = hDnaFromSeq(database, seqName, winStart, winEnd, dnaLower); if (isRc) reverseComplement(seq->dna, seq->size); if (defaultUpper) touppers(seq->dna); AllocArray(colors, winSize); for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { char *track = tdb->track; char *table = tdb->table; struct featureBits *fbList = NULL, *fb; struct customTrack *ct = lookupCt(track); if (sameString(USER_PSL_TRACK_NAME, table) || ct != NULL || ( tdbVisLimitedByAncestors(cart,tdb,TRUE,TRUE) != tvHide && forestHasUnderstandableTrack(database, tdb) ) ) { char buf[256]; int r,g,b; /* to save a LOT of time, don't fetch track features unless some * coloring/formatting has been specified for them. */ boolean hasSettings = FALSE; safef(buf, sizeof(buf), "%s_u", track); hasSettings |= cgiBoolean(buf); safef(buf, sizeof(buf), "%s_b", track); hasSettings |= cgiBoolean(buf); safef(buf, sizeof(buf), "%s_i", track); hasSettings |= cgiBoolean(buf); safef(buf, sizeof(buf), "%s_case", track); hasSettings |= cgiBoolean(buf); safef(buf, sizeof(buf), "%s_red", track); hasSettings |= (cgiOptionalInt(buf, 0) != 0); safef(buf, sizeof(buf), "%s_green", track); hasSettings |= (cgiOptionalInt(buf, 0) != 0); safef(buf, sizeof(buf), "%s_blue", track); hasSettings |= (cgiOptionalInt(buf, 0) != 0); if (! hasSettings) continue; if (sameString(USER_PSL_TRACK_NAME, track)) { struct hTableInfo *hti = htiForUserPsl(); struct bedFilter *bf; struct bed *bedList, *bedList2; AllocVar(bf); bedList = bedFromUserPsl(); bedList2 = bedFilterListInRange(bedList, bf, seqName, winStart, winEnd); fbList = fbFromBed(database, track, hti, bedList2, winStart, winEnd, TRUE, FALSE); bedFreeList(&bedList); bedFreeList(&bedList2); } else if (ct != NULL) { struct hTableInfo *hti = ctToHti(ct); struct bedFilter *bf; struct bed *bedList2, *ctBedList = NULL; AllocVar(bf); if (ct->dbTrack) { struct bed *bed; int fieldCount = ct->fieldCount; char query[512]; int rowOffset; char **row; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct sqlResult *sr = NULL; sqlSafef(query, sizeof(query), "select * from %s", ct->dbTableName); sr = hRangeQuery(conn, ct->dbTableName, seqName, winStart, winEnd, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+rowOffset, fieldCount); if (bf == NULL || bedFilterOne(bf, bed)) { struct bed *copy = cloneBed(bed); slAddHead(&ctBedList, copy); } } sqlFreeResult(&sr); hFreeConn(&conn); } else { ctBedList = ct->bedList; } bedList2 = bedFilterListInRange(ctBedList, bf, seqName, winStart, winEnd); fbList = fbFromBed(database, track, hti, bedList2, winStart, winEnd, TRUE, FALSE); bedFreeList(&bedList2); if (!ct->bedList) bedFreeList(&ctBedList); } else { if (tdb->subtracks) { struct slRef *refLeaves = trackDbListGetRefsToDescendantLeaves(tdb->subtracks); struct slRef *refLeaf = NULL; while ((refLeaf = slPopHead(&refLeaves)) != NULL) { struct trackDb *tdbLeaf = refLeaf->val; if (tdbVisLimitedByAncestors(cart,tdbLeaf,TRUE,TRUE) != tvHide && fbUnderstandTrack(database, tdbLeaf->table) && !dnaIgnoreTrack(tdbLeaf->table)) { struct featureBits *fbLeafList = fbGetRange(database, tdbLeaf->table, seqName, winStart, winEnd); if (fbLeafList != NULL) fbList = slCat(fbList,fbLeafList); } freeMem(refLeaf); } } else fbList = fbGetRange(database, tdb->table, seqName, winStart, winEnd); } /* Flip underline/italic/bold bits. */ getDnaHandleBits(track, "u", uBits, winStart, winEnd, isRc, fbList); getDnaHandleBits(track, "b", bBits, winStart, winEnd, isRc, fbList); getDnaHandleBits(track, "i", iBits, winStart, winEnd, isRc, fbList); /* Toggle case if necessary. */ safef(buf, sizeof buf, "%s_case", track); if (cgiBoolean(buf)) { for (fb = fbList; fb != NULL; fb = fb->next) { DNA *dna; int start = fb->start - winStart; int end = fb->end - winStart; int size = fb->end - fb->start; if (isRc) reverseIntRange(&start, &end, seq->size); dna = seq->dna + start; if (defaultUpper) toLowerN(dna, size); else toUpperN(dna, size); } } /* Add in RGB values if necessary. */ safef(buf, sizeof buf, "%s_red", track); r = cartInt(cart, buf); safef(buf, sizeof buf, "%s_green", track); g = cartInt(cart, buf); safef(buf, sizeof buf, "%s_blue", track); b = cartInt(cart, buf); if (r != 0 || g != 0 || b != 0) { for (fb = fbList; fb != NULL; fb = fb->next) { int s = fb->start - winStart; int e = fb->end - winStart; if (isRc) reverseIntRange(&s, &e, winEnd - winStart); addColorToRange(r, g, b, colors, s, e); } } } } cfm = cfmNew(0, lineWidth, FALSE, FALSE, stdout, 0); for (i=0; i<seq->size; ++i) { struct rgbColor *color = colors+i; int c = (color->r<<16) + (color->g<<8) + color->b; cfmOutExt(cfm, seq->dna[i], c, bitReadOne(uBits, i), bitReadOne(bBits, i), bitReadOne(iBits, i)); } cfmFree(&cfm); freeDnaSeq(&seq); bitFree(&uBits); bitFree(&iBits); bitFree(&bBits); } void medlineLinkedTermLine(char *title, char *text, char *search, char *keyword) /* Produce something that shows up on the browser as * TITLE: value * with the value hyperlinked to medline using a specified search term. */ { char *encoded = cgiEncode(search); char *encodedKeyword = cgiEncode(keyword); printf("<B>%s:</B> ", title); if (sameWord(text, "n/a") || sameWord(text, "none")) printf("n/a<BR>\n"); else { printf("<A HREF=\""); printEntrezPubMedPureSearchUrl(stdout, encoded, encodedKeyword); printf("\" TARGET=_blank>%s</A><BR>\n", text); } freeMem(encoded); } void medlineLinkedLine(char *title, char *text, char *search) /* Produce something that shows up on the browser as * TITLE: value * with the value hyperlinked to medline. */ { char *encoded = cgiEncode(search); printf("<B>%s:</B> ", title); if (sameWord(text, "n/a")) printf("n/a<BR>\n"); else { printf("<A HREF=\""); printEntrezPubMedUrl(stdout, encoded); printf("\" TARGET=_blank>%s</A><BR>\n", text); } freeMem(encoded); } void medlineProductLinkedLine(char *title, char *text) /* Produce something that shows up on the browser as * TITLE: value * with the value hyperlinked to medline. * Replaces commas in the product name with spaces, as commas sometimes * interfere with PubMed search */ { subChar(text, ',', ' '); medlineLinkedLine(title, text, text); } void appendAuthor(struct dyString *dy, char *gbAuthor, int len) /* Convert from Kent,W.J. to Kent WJ and append to dy. * gbAuthor gets eaten in the process. * Also strip web URLs since Entrez doesn't like those. */ { char buf[2048]; char *ptr; if (len >= sizeof(buf)) warn("author %s too long to process", gbAuthor); else { memcpy(buf, gbAuthor, len); buf[len] = 0; stripChar(buf, '.'); subChar(buf, ',' , ' '); if ((ptr = strstr(buf, " http://")) != NULL) *ptr = 0; dyStringAppend(dy, buf); dyStringAppend(dy, " "); } } void gbToEntrezAuthor(char *authors, struct dyString *dy) /* Convert from Genbank author format: * Kent,W.J., Haussler,D. and Zahler,A.M. * to Entrez search format: * Kent WJ,Haussler D,Zahler AM */ { char *s = authors, *e; /* Parse first authors, which will be terminated by '.,' */ while ((e = strstr(s, ".,i ")) != NULL) { int len = e - s + 1; appendAuthor(dy, s, len); s += len+2; } if ((e = strstr(s, " and")) != NULL) { int len = e - s; appendAuthor(dy, s, len); s += len+4; } if ((s = skipLeadingSpaces(s)) != NULL && s[0] != 0) { int len = strlen(s); appendAuthor(dy, s, len); } } /* --- !!! Riken code is under development Fan. 4/16/02 */ void printRikenInfo(char *acc, struct sqlConnection *conn ) /* Print Riken annotation info */ { struct sqlResult *sr; char **row; char query[512]; char *seqid, *accession, *comment; // char *qualifier, *anntext, *datasrc, *srckey, *href, *evidence; accession = acc; sqlSafef(query, sizeof(query), "select seqid from rikenaltid where altid='%s';", accession); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { seqid=cloneString(row[0]); sqlSafef(query, sizeof(query), "select Qualifier, Anntext, Datasrc, Srckey, Href, Evidence " "from rikenann where seqid='%s';", seqid); sqlFreeResult(&sr); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); while (row !=NULL) { // qualifier = row[0]; unused variable // anntext = row[1]; unused variable // datasrc = row[2]; unused variable // srckey = row[3]; unused variable // href = row[4]; unused variable // evidence = row[5]; unused variable row = sqlNextRow(sr); } sqlSafef(query, sizeof(query), "select comment from rikenseq where id='%s';", seqid); sqlFreeResult(&sr); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { comment = row[0]; printf("<B>Riken/comment:</B> %s<BR>\n",comment); } } } void printGeneCards(char *geneName) /* Print out a link to GeneCards (Human only). */ { if (startsWith("hg", database) && isNotEmpty(geneName)) { printf("<B>GeneCards:</B> " "<A HREF = \"http://www.genecards.org/cgi-bin/cardsearch.pl?" "search=%s\" TARGET=_blank>%s</A><BR>\n", geneName, geneName); } } int getImageId(struct sqlConnection *conn, char *acc) /* get the image id for a clone, or 0 if none */ { int imageId = 0; if (sqlTableExists(conn, imageCloneTable)) { struct sqlResult *sr; char **row; char query[128]; sqlSafef(query, sizeof(query), "select imageId from %s where acc = '%s'",imageCloneTable, acc); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) imageId = sqlUnsigned(row[0]); sqlFreeResult(&sr); } return imageId; } void htcDisplayMrna(char *acc) /* Display mRNA available from genback or seq table.. */ { struct dnaSeq *seq = hGenBankGetMrna(database, acc, NULL); if (seq == NULL) errAbort("mRNA sequence %s not found", acc); cartHtmlStart("mRNA sequence"); printf("<PRE><TT>"); faWriteNext(stdout, seq->name, seq->dna, seq->size); printf("</TT></PRE>"); dnaSeqFree(&seq); } static int getEstTranscriptionDir(struct sqlConnection *conn, struct psl *psl) /* get the direction of transcription for an EST; return splice support count */ { char query[256], estOrient[64]; sqlSafef(query, sizeof(query), "select intronOrientation from %s.estOrientInfo where chrom = '%s' and chromStart = %d and name = '%s'", database, psl->tName, psl->tStart, psl->qName); if (sqlQuickQuery(conn, query, estOrient, sizeof(estOrient)) != NULL) return sqlSigned(estOrient) * ((psl->strand[0] == '+') ? 1 : -1); else return 0; } static struct gbWarn *checkGbWarn(struct sqlConnection *conn, char *acc) /* check if there is a gbWarn entry for this accession, return NULL if none */ { struct gbWarn *gbWarn = NULL; if (sqlTableExists(conn, gbWarnTable)) gbWarn = sqlQueryObjs(conn, (sqlLoadFunc)gbWarnLoad, sqlQuerySingle, "SELECT * FROM %s WHERE acc = \"%s\"", gbWarnTable, acc); return gbWarn; } static void printGbWarn(char *acc, struct gbWarn *gbWarn) /* print descriptive information about an accession in the gbWarn table */ { char *msg = NULL; switch (gbWarn->reason) { case gbWarnInvitroNorm: msg = "is from the InVitroGen/Genoscope full-length library. Some of the entries " "associated with this dataset appear to have been aligned to the reference " "genome and the sequences subsequently modified to match the genome. This " "process may have resulted in apparent high-quality alignments to pseudogenes."; break; case gbWarnAthRage: msg = "is from the Athersys RAGE library. These sequences were created by inducing expression and may not " "be an indication of in vivo expression."; break; case gbWarnOrestes: msg = "is from an ORESTES library. This protocol includes a PCR step subject to genomic contamination."; break; } assert(msg != NULL); char *msg2= "Care should be taken in using alignments of this sequence as evidence of transcription."; printf("<B>Warning:<span style='color:red;'> %s %s %s</span></B><BR>\n", acc, msg, msg2); } static void printRnaSpecs(struct trackDb *tdb, char *acc, struct psl *psl) /* Print auxiliarry info on RNA. */ { struct dyString *dy = newDyString(1024); struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2= hAllocConn(database); struct sqlResult *sr; char **row; char rgdEstId[512]; char query[256]; char *type,*direction,*orgFullName,*library,*clone,*sex,*tissue, *development,*cell,*cds,*description, *author,*geneName, *date,*productName; // char *source; unused variable // int seqSize,fileSize; unused variables // long fileOffset; unused variable // char *extFile; unused variable boolean hasVersion = hHasField(database, gbCdnaInfoTable, "version"); boolean haveGbSeq = sqlTableExists(conn, gbSeqTable); char *seqTbl = haveGbSeq ? gbSeqTable : "seq"; char *version = NULL; struct trackDb *tdbRgdEst; char *chrom = cartString(cart, "c"); int start = cartInt(cart, "o"); int end = cartUsualInt(cart, "t",0); struct gbWarn *gbWarn = checkGbWarn(conn, acc); /* This sort of query and having to keep things in sync between * the first clause of the select, the from clause, the where * clause, and the results in the row ... is really tedious. * One of my main motivations for going to a more object * based rather than pure relational approach in general, * and writing 'autoSql' to help support this. However * the pure relational approach wins for pure search speed, * and these RNA fields are searched. So it looks like * the code below stays. Be really careful when you modify * it. * * Uses the gbSeq table if available, otherwise use seq for older databases. */ sqlDyStringPrintf(dy, "select g.type,g.direction," "so.name,o.name,l.name,m.name," "se.name,t.name,dev.name,ce.name,cd.name," "des.name,a.name,gene.name,p.name," "gbS.size,g.moddate,gbS.gbExtFile,gbS.file_offset,gbS.file_size "); /* If the gbCdnaInfoTAble table has a "version" column then will show it */ if (hasVersion) { sqlDyStringPrintf(dy, ", g.version "); } sqlDyStringPrintf(dy, " from %s g,%s gbS,%s so,%s o,%s l,%s m,%s se,%s t," "%s dev,%s ce,%s cd,%s des,%s a,%s gene,%s p" " where g.acc = '%s' and g.id = gbS.id ", gbCdnaInfoTable,seqTbl, sourceTable, organismTable, libraryTable, mrnaCloneTable, sexTable, tissueTable, developmentTable, cellTable, cdsTable, descriptionTable, authorTable, geneNameTable, productNameTable, acc); sqlDyStringPrintf(dy, "and g.source = so.id and g.organism = o.id " "and g.library = l.id and g.mrnaClone = m.id " "and g.sex = se.id and g.tissue = t.id " "and g.development = dev.id and g.cell = ce.id " "and g.cds = cd.id and g.description = des.id " "and g.author = a.id and g.geneName = gene.id " "and g.productName = p.id"); sr = sqlMustGetResult(conn, dy->string); row = sqlNextRow(sr); if (row != NULL) { type=row[0];direction=row[1]; // source=row[2]; unused variable orgFullName=row[3];library=row[4];clone=row[5]; sex=row[6];tissue=row[7];development=row[8];cell=row[9];cds=row[10];description=row[11]; author=row[12];geneName=row[13];productName=row[14]; // seqSize = sqlUnsigned(row[15]); unused variable date = row[16]; // ext_file = row[17]; unused variable // fileOffset=sqlUnsigned(row[18]); unused variable // fileSize=sqlUnsigned(row[19]); unused variable boolean isEst = sameWord(type, "est"); if (hasVersion) { version = row[20]; } /* Now we have all the info out of the database and into nicely named * local variables. There's still a few hoops to jump through to * format this prettily on the web with hyperlinks to NCBI. */ printf("<H2>Information on %s <A HREF=\"", type); if (isEst) printEntrezEstUrl(stdout, acc); else printEntrezNucleotideUrl(stdout, acc); printf("\" TARGET=_blank>%s</A></H2>\n", acc); printf("<B>Description:</B> %s<BR>\n", description); if (gbWarn != NULL) printGbWarn(acc, gbWarn); medlineLinkedLine("Gene", geneName, geneName); medlineProductLinkedLine("Product", productName); dyStringClear(dy); gbToEntrezAuthor(author, dy); medlineLinkedLine("Author", author, dy->string); printf("<B>Organism:</B> "); printf("<A href=\"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1\" TARGET=_blank>", cgiEncode(orgFullName)); printf("%s</A><BR>\n", orgFullName); printf("<B>Tissue:</B> %s<BR>\n", tissue); printf("<B>Development stage:</B> %s<BR>\n", development); printf("<B>Cell line:</B> %s<BR>\n", cell); printf("<B>Sex:</B> %s<BR>\n", sex); printf("<B>Library:</B> %s<BR>\n", library); printf("<B>Clone:</B> %s<BR>\n", clone); if (isEst) { printf("<B>Read direction: </B>"); if (direction[0] != '0') printf("%s' (guessed from GenBank description)<BR>\n", direction); else printf("unknown (can't guess from GenBank description)<BR>"); } else printf("<B>CDS:</B> %s<BR>\n", cds); printf("<B>Date:</B> %s<BR>\n", date); if (hasVersion) { printf("<B>Version:</B> %s<BR>\n", version); } /* print RGD EST Report link if it is Rat genome and it has a link to RGD */ if (sameWord(organism, "Rat")) { if (hTableExists(database, "rgdEstLink")) { sqlSafef(query, sizeof(query), "select id from %s.rgdEstLink where name = '%s';", database, acc); if (sqlQuickQuery(conn2, query, rgdEstId, sizeof(rgdEstId)) != NULL) { tdbRgdEst = hashFindVal(trackHash, "rgdEst"); printf("<B>RGD EST Report: "); printf("<A HREF=\"%s%s\" target=_blank>", tdbRgdEst->url, rgdEstId); printf("RGD:%s</B></A><BR>\n", rgdEstId); } } } if (isEst && hTableExists(database, "estOrientInfo") && (psl != NULL)) { int estOrient = getEstTranscriptionDir(conn2, psl); if (estOrient != 0) printf("<B>EST transcribed from %c strand </B>(supported by %d splice sites).<BR>\n", (estOrient > 0 ? '+' : '-' ), abs(estOrient)); } if (hGenBankHaveSeq(database, acc, NULL)) { printf("<B>%s sequence:</B> ", type); hgcAnchorSomewhere("htcDisplayMrna", acc, tdb->track, seqName); printf("%s</A><BR>\n", acc); } } else { warn("Couldn't find %s in %s table", gbCdnaInfoTable, acc); } if (end != 0 && differentString(chrom,"0") && isNotEmpty(chrom)) { printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, chrom, start+1, end); printf("%s:%d-%d</A><BR>\n", chrom, start+1, end); } gbWarnFree(&gbWarn); sqlFreeResult(&sr); freeDyString(&dy); hFreeConn(&conn); hFreeConn(&conn2); } static boolean isPslToPrintByClick(struct psl *psl, int startFirst, boolean isClicked) /* Determine if a psl should be printed based on if it was or was not the one that was clicked * on. */ { return ((psl->tStart == startFirst) && sameString(psl->tName, seqName)) == isClicked; } void printAlignmentsSimple(struct psl *pslList, int startFirst, char *hgcCommand, char *tableName, char *itemIn) /* Print list of mRNA alignments, don't add extra textual link when * doesn't honor hgcCommand. */ { struct psl *psl; int aliCount = slCount(pslList); boolean isClicked; if (pslList == NULL || tableName == NULL) return; boolean showEvery = sameString(itemIn, "PrintAllSequences"); if (!showEvery && (aliCount > 1)) printf("The alignment you clicked on is first in the table below.<BR>\n"); printf("<PRE><TT>"); if (startsWith("chr", pslList->tName)) printf("BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END QUERY START END TOTAL\n"); else printf("BROWSER | SIZE IDENTITY SCAFFOLD STRAND START END QUERY START END TOTAL\n"); printf("-----------------------------------------------------------------------------------------------------\n"); for (isClicked = 1; isClicked >= 0; isClicked -= 1) { for (psl = pslList; psl != NULL; psl = psl->next) { if (isPslToPrintByClick(psl, startFirst, isClicked)) { char otherString[512]; char *qName = itemIn; if (sameString(itemIn, "PrintAllSequences")) qName = psl->qName; safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, tableName); printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">browser</A> | ", hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd); hgcAnchorWindow(hgcCommand, qName, psl->tStart, psl->tEnd, otherString, psl->tName); printf("%5d %5.1f%% %9s %s %9d %9d %20s %5d %5d %5d</A>", psl->match + psl->misMatch + psl->repMatch, 100.0 - pslCalcMilliBad(psl, TRUE) * 0.1, skipChr(psl->tName), psl->strand, psl->tStart + 1, psl->tEnd, psl->qName, psl->qStart+1, psl->qEnd, psl->qSize); printf("\n"); } } } printf("</TT></PRE>"); } void printAlignmentsExtra(struct psl *pslList, int startFirst, char *hgcCommand, char *hgcCommandInWindow, char *tableName, char *itemIn) /* Print list of mRNA alignments with special "in window" alignment function. */ { if (pslList == NULL || tableName == NULL) return; printAlignmentsSimple(pslList, startFirst, hgcCommand, tableName, itemIn); struct psl *psl = pslList; for (psl = pslList; psl != NULL; psl = psl->next) { if ( pslTrimToTargetRange(psl, winStart, winEnd) != NULL && !startsWith("xeno", tableName) && !(startsWith("user", tableName) && pslIsProtein(psl)) && psl->tStart == startFirst && sameString(psl->tName, seqName) ) { char otherString[512]; safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, tableName); hgcAnchorSomewhere(hgcCommandInWindow, itemIn, otherString, psl->tName); printf("<BR>View details of parts of alignment within browser window</A>.<BR>\n"); } } } void printAlignments(struct psl *pslList, int startFirst, char *hgcCommand, char *tableName, char *itemIn) /* Print list of mRNA alignments. */ { printAlignmentsExtra(pslList, startFirst, hgcCommand, "htcCdnaAliInWindow", tableName, itemIn); } static struct psl *getAlignmentsTName(struct sqlConnection *conn, char *table, char *acc, char *tName) /* get the list of alignments for the specified acc and tName (if given). */ { struct sqlResult *sr = NULL; char **row; struct psl *psl, *pslList = NULL; boolean hasBin; char splitTable[HDB_MAX_TABLE_STRING]; char query[1024]; if (!hFindSplitTable(database, seqName, table, splitTable, sizeof splitTable, &hasBin)) errAbort("can't find table %s or %s_%s", table, seqName, table); if (isNotEmpty(tName)) sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s'", splitTable, acc, tName); else sqlSafef(query, sizeof(query), "select * from %s where qName = '%s'", splitTable, acc); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row+hasBin); slAddHead(&pslList, psl); } sqlFreeResult(&sr); slReverse(&pslList); return pslList; } struct psl *getAlignments(struct sqlConnection *conn, char *table, char *acc) /* get the list of alignments for the specified acc */ { return getAlignmentsTName(conn, table, acc, NULL); } struct psl *loadPslRangeT(char *table, char *qName, char *tName, int tStart, int tEnd) /* Load a list of psls given qName tName tStart tEnd */ { struct sqlResult *sr = NULL; char **row; struct psl *psl = NULL, *pslList = NULL; boolean hasBin; char splitTable[HDB_MAX_TABLE_STRING]; char query[256]; struct sqlConnection *conn = hAllocConn(database); if (!hFindSplitTable(database, seqName, table, splitTable, sizeof splitTable, &hasBin)) errAbort("loadPslRangeT track %s not found", table); sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s' and tEnd > %d and tStart < %d", splitTable, qName, tName, tStart, tEnd); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row+hasBin); slAddHead(&pslList, psl); } sqlFreeResult(&sr); slReverse(&pslList); hFreeConn(&conn); return pslList; } void doHgRna(struct trackDb *tdb, char *acc) /* Click on an individual RNA. */ { char *track = tdb->track; char *table = tdb->table; struct sqlConnection *conn = hAllocConn(database); char *type; int start = cartInt(cart, "o"); struct psl *pslList = NULL; if (sameString("xenoMrna", track) || sameString("xenoBestMrna", track) || sameString("xenoEst", track) || sameString("sim4", track) ) { char temp[256]; safef(temp, sizeof temp, "non-%s RNA", organism); type = temp; } else if ( sameWord("blatzHg17KG", track) ) { type = "Human mRNA"; } else if (stringIn("estFiltered",track)) { type = "EST"; } else if (stringIn("est", track) || stringIn("Est", track)) { type = "EST"; // table = "all_est"; // Should fall out of wash now } else if (startsWith("psu", track)) { type = "Pseudo & Real Genes"; table = "psu"; } else if (sameWord("xenoBlastzMrna", track) ) { type = "Blastz to foreign mRNA"; } else if (startsWith("mrnaBlastz",track )) { type = "mRNA"; } else if (startsWith("pseudoMrna",track) || startsWith("pseudoGeneLink",track)) { type = "mRNA"; table = "pseudoMrna"; } else if (startsWith("celeraMrna",track)) { type = "mRNA"; } else if (startsWith("all_mrnaFiltered",track)) { type = "mRNA"; } else { type = "mRNA"; // table = "all_mrna"; // should fall out of wash now } /* Print non-sequence info. */ cartWebStart(cart, database, "%s", acc); printRnaSpecs(tdb, acc, pslList); /* Get alignment info. */ pslList = getAlignments(conn, table, acc); if (pslList == NULL) { /* this was not actually a click on an aligned item -- we just * want to display RNA info, so leave here */ hFreeConn(&conn); htmlHorizontalLine(); printf("mRNA %s alignment does not meet minimum alignment criteria on this assembly.", acc); return; } htmlHorizontalLine(); printf("<H3>%s/Genomic Alignments</H3>", type); if (startsWith("mrnaBlastz",tdb->table)) slSort(&pslList, pslCmpScoreDesc); printAlignments(pslList, start, "htcCdnaAli", table, acc); printTrackHtml(tdb); hFreeConn(&conn); } void printPslFormat(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *subType) /* Handles click in affyU95 or affyU133 tracks */ { struct psl *pslList = getAlignments(conn, tdb->table, item); struct psl *psl; char *face = "Times"; /* specifies font face to use */ char *fsize = "+1"; /* specifies font size */ /* check if there is an alignment available for this sequence. This checks * both genbank sequences and other sequences in the seq table. If so, * set it up so they can click through to the alignment. */ if (hGenBankHaveSeq(database, item, NULL)) { printf("<H3>%s/Genomic Alignments</H3>", item); printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); } else { /* print out the psls */ printf("<PRE><TT>"); printf("<span style='font-family:%s; font-size:%s;'>\n", face, fsize); for (psl = pslList; psl != NULL; psl = psl->next) { pslOutFormat(psl, stdout, '\n', '\n'); } printf("</span></TT></PRE>\n"); } pslFreeList(&pslList); } void doAffy(struct trackDb *tdb, char *item, char *itemForUrl) /* Display information for Affy tracks*/ { char *dupe, *type, *words[16]; char *orthoTable = trackDbSetting(tdb, "orthoTable"); char *otherDb = trackDbSetting(tdb, "otherDb"); int wordCount; int start = cartInt(cart, "o"); char query[256]; char **row; struct sqlResult *sr = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); if (itemForUrl == NULL) itemForUrl = item; dupe = cloneString(tdb->type); genericHeader(tdb, item); wordCount = chopLine(dupe, words); printCustomUrl(tdb, itemForUrl, item == itemForUrl); /* If this is the affyZebrafish track, check for human ortholog information */ if (sameString("affyZebrafish", tdb->table)) { if (orthoTable != NULL && hTableExists(database, orthoTable)) { sqlSafef(query, sizeof(query), "select geneSymbol, description from %s where name = '%s' ", orthoTable, item); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<P><HR ALIGN=\"CENTER\"></P>\n<TABLE>\n"); printf("<TR><TH ALIGN=left><H2>Human %s Ortholog:</H2></TH><TD>%s</TD></TR>\n", otherDb, row[0]); printf("<TR><TH ALIGN=left>Ortholog Description:</TH><TD>%s</TD></TR>\n",row[1]); printf("</TABLE>\n"); } } } if (wordCount > 0) { type = words[0]; if (sameString(type, "psl")) { char *subType = "."; if (wordCount > 1) subType = words[1]; printPslFormat(conn2, tdb, item, start, subType); } } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); hFreeConn(&conn2); } void doZfishRHmap(struct trackDb *tdb, char *itemName) /* Put up Radiation Hybrid map information for Zebrafish */ { char *dupe, *type, *words[16]; char query[256]; struct sqlResult *sr = NULL; char **row = NULL; struct rhMapZfishInfo *rhInfo = NULL; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn1 = hAllocConn(database); boolean rhMapInfoExists = sqlTableExists(conn, "rhMapZfishInfo"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); genericHeader(tdb, itemName); /* Print out RH map information if available */ if (rhMapInfoExists) { sqlSafef(query, sizeof query, "SELECT * FROM rhMapZfishInfo WHERE name = '%s'", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { rhInfo = rhMapZfishInfoLoad(row); if (rhInfo != NULL) { printf("<H2>Information on %s </H2>\n", itemName); if (!sameString(rhInfo->zfinId, "")) { printf("<H3>"); printCustomUrl(tdb, rhInfo->zfinId, TRUE); printf("</H3>\n"); } printf("<P><HR ALIGN=\"CENTER\"></P>\n<TABLE>\n"); printf("<TR><TH ALIGN=left>Linkage group:</TH><TD>%s</TD></TR>\n", rhInfo->linkageGp); printf("<TR><TH ALIGN=left>Position on linkage group:</TH><TD>%d</TD></TR>\n", rhInfo->position); printf("<TR><TH ALIGN=left>Distance (cR):</TH><TD>%d</TD></TR>\n", rhInfo->distance); printf("<TR><TH ALIGN=left>Marker type:</TH><TD>%s</TD></TR>\n", rhInfo->markerType); printf("<TR><TH ALIGN=left>Marker source:</TH><TD>%s</TD></TR>\n", rhInfo->source); printf("<TR><TH ALIGN=left>Mapping institution:</TH><TD>%s</TD></TR>\n", rhInfo->mapSite); printf("<TR><TH ALIGN=left>Forward Primer:</TH><TD>%s</TD></TR>\n", rhInfo->leftPrimer); printf("<TR><TH ALIGN=left>Reverse Primer:</TH><TD>%s</TD></TR>\n", rhInfo->rightPrimer); printf("</TABLE>\n"); } } } dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 0) { type = words[0]; if (sameString(type, "psl")) { char *subType = "."; if (wordCount > 1) subType = words[1]; printPslFormat(conn1, tdb, itemName, start, subType); } } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); hFreeConn(&conn1); } void doRikenRna(struct trackDb *tdb, char *item) /* Put up Riken RNA stuff. */ { char query[512]; struct sqlResult *sr; char **row; struct sqlConnection *conn = sqlConnect("mgsc"); genericHeader(tdb, item); sqlSafef(query, sizeof query, "select * from rikenMrna where qName = '%s'", item); sr = sqlGetResult(conn, query); printf("<PRE><TT>\n"); printf("#match\tmisMatches\trepMatches\tnCount\tqNumInsert\tqBaseInsert\ttNumInsert\tBaseInsert\tstrand\tqName\tqSize\tqStart\tqEnd\ttName\ttSize\ttStart\ttEnd\tblockCount\tblockSizes\tqStarts\ttStarts\n"); while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row+1); pslTabOut(psl, stdout); } printf("</TT></PRE>\n"); sqlDisconnect(&conn); printTrackHtml(tdb); } void doYaleTars(struct trackDb *tdb, char *item, char *itemForUrl) /* Display information for Affy tracks*/ { char *dupe, *type, *words[16], *chrom = NULL, *strand = NULL; char *item2 = NULL; int wordCount, end = 0; int start = cartInt(cart, "o"); char query[256]; char **row; struct sqlResult *sr = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); if (itemForUrl == NULL) { if (startsWith("TAR", item)) { /* Remove TAR prefix from item */ item2 = strchr(item, 'R'); item2++; itemForUrl = item2; } else itemForUrl = item; } dupe = cloneString(tdb->type); genericHeader(tdb, item); wordCount = chopLine(dupe, words); printCustomUrl(tdb, itemForUrl, item == itemForUrl); sqlSafef(query, sizeof(query), "select tName, tEnd, strand from %s where qName='%s' and tStart=%d;", tdb->table, item, start); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); /* load PSL into struct */ if (row != NULL) { chrom = cloneString(row[0]); end = sqlUnsigned(row[1]); strand = cloneString(row[2]); } printPos(chrom, start, end, strand, TRUE, item); if (wordCount > 0) { type = words[0]; if (sameString(type, "psl")) { char *subType = "."; if (wordCount > 1) subType = words[1]; printPslFormat(conn2, tdb, item, start, subType); } } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); hFreeConn(&conn2); } void printPcrTargetMatch(struct targetDb *target, struct psl *tpsl, boolean mustGetItem) /* Show the non-genomic target PCR result and its genomic mapping. */ { char *acc = pcrResultItemAccession(tpsl->tName); char *name = pcrResultItemName(tpsl->tName); char niceName[256]; if (name == NULL || sameString(acc, name)) safecpy(niceName, sizeof(niceName), acc); else safef(niceName, sizeof(niceName), "%s (%s)", name, acc); printf("<B>Position in %s:</B> <A HREF=\"%s?%s&db=%s&position=%s\">%s</A>" ":%d-%d<BR>\n", target->description, hgTracksName(), cartSidUrlString(cart), database, acc, niceName, tpsl->tStart+1, tpsl->tEnd); printf("<B>Size in %s:</B> %d<BR>\n", niceName, tpsl->tEnd - tpsl->tStart); if (tpsl->strand[0] == '-') printf(" " "<EM>Warning: the match is on the reverse strand of %s</EM><BR>\n", niceName); struct psl *itemPsl = NULL, *otherPsls = NULL, *gpsl; int itemStart = cartInt(cart, "o"); int itemEnd = cartInt(cart, "t"); int rowOffset = hOffsetPastBin(database, seqName, target->pslTable); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[2048]; sqlSafef(query, sizeof(query), "select * from %s where qName = '%s'", target->pslTable, acc); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { gpsl = pslLoad(row+rowOffset); struct psl *pslTrimmed = pslTrimToQueryRange(gpsl, tpsl->tStart, tpsl->tEnd); if (sameString(gpsl->tName, seqName) && ((gpsl->tStart == itemStart && gpsl->tEnd == itemEnd) || (pslTrimmed->tStart == itemStart && pslTrimmed->tEnd == itemEnd))) itemPsl = pslTrimmed; else slAddHead(&otherPsls, pslTrimmed); pslFree(&gpsl); } hFreeConn(&conn); if (mustGetItem && itemPsl == NULL) errAbort("Did not find record for amplicon in %s at %s:%d-%d", niceName, seqName, itemStart, itemEnd); char strand[2]; strand[1] = '\0'; if (itemPsl != NULL) { if (itemPsl->strand[1] == '\0') strand[0] = itemPsl->strand[0]; else if (itemPsl->strand[0] != itemPsl->strand[1]) strand[0] = '-'; else strand[0] = '+'; if (itemPsl != NULL) printPosOnChrom(itemPsl->tName, itemPsl->tStart, itemPsl->tEnd, strand, FALSE, tpsl->tName); } slSort(&otherPsls, pslCmpTarget); if (itemPsl != NULL && otherPsls != NULL) printf("<B>Other matches in genomic alignments of %s:</B><BR>\n", niceName); for (gpsl = otherPsls; gpsl != NULL; gpsl = gpsl->next) { if (gpsl->strand[1] == '\0') strand[0] = gpsl->strand[0]; else if (gpsl->strand[0] != gpsl->strand[1]) strand[0] = '-'; else strand[0] = '+'; printPosOnChrom(gpsl->tName, gpsl->tStart, gpsl->tEnd, strand, FALSE, tpsl->tName); } pslFree(&itemPsl); pslFreeList(&otherPsls); } static void upperMatch(char *dna, char *primer, int size) /* Uppercase DNA where it matches primer. -- copied from gfPcrLib.c. */ { int i; for (i=0; i<size; ++i) { if (dna[i] == primer[i]) dna[i] = toupper(dna[i]); } } void printPcrSequence(struct targetDb *target, struct psl *psl, char *fPrimer, char *rPrimer) /* Print the amplicon sequence (as on hgPcr results page). */ { int productSize = psl->tEnd - psl->tStart; char *ffPrimer = cloneString(fPrimer); char *rrPrimer = cloneString(rPrimer); int rPrimerSize = strlen(rPrimer); struct dnaSeq *seq; if (target != NULL) { /* Use seq+extFile if specified; otherwise just retrieve from seqFile. */ if (isNotEmpty(target->seqTable) && isNotEmpty(target->extFileTable)) { struct sqlConnection *conn = hAllocConn(database); seq = hDnaSeqGet(database, psl->tName, target->seqTable, target->extFileTable); hFreeConn(&conn); char *dna = cloneStringZ(seq->dna + psl->tStart, productSize); freeMem(seq->dna); seq->dna = dna; } else { struct twoBitFile *tbf = twoBitOpen(target->seqFile); seq = twoBitReadSeqFrag(tbf, psl->tName, psl->tStart, psl->tEnd); twoBitClose(&tbf); } } else seq = hChromSeq(database, psl->tName, psl->tStart, psl->tEnd); char *dna = seq->dna; tolowers(dna); if (psl->strand[0] == '-') reverseComplement(dna, productSize); printf("<TT><PRE>"); /* The rest of this is loosely copied from gfPcrLib.c:outputFa(): */ char *tNameForPos = (target != NULL ? pcrResultItemAccession(psl->tName) : psl->tName); printf("><A HREF=\"%s?%s&db=%s&position=%s", hgTracksName(), cartSidUrlString(cart), database, tNameForPos); if (target == NULL) printf(":%d-%d", psl->tStart+1, psl->tEnd); printf("\">%s:%d%c%d</A> %dbp %s %s\n", psl->tName, psl->tStart+1, psl->strand[0], psl->tEnd, productSize, fPrimer, rPrimer); /* Flip reverse primer to be in same direction and case as sequence, to * compare with sequence: */ reverseComplement(rrPrimer, rPrimerSize); tolowers(rrPrimer); tolowers(ffPrimer); /* Capitalize where sequence and primer match, and write out sequence. */ upperMatch(dna, ffPrimer, strlen(ffPrimer)); upperMatch(dna + productSize - rPrimerSize, rrPrimer, rPrimerSize); faWriteNext(stdout, NULL, dna, productSize); printf("</PRE></TT>"); } void doPcrResult(char *track, char *item) /* Process click on PCR of user's primers. */ { struct trackDb *tdb = pcrResultFakeTdb(); char *pslFileName, *primerFileName; struct targetDb *target; cartWebStart(cart, database, "PCR Results"); if (! pcrResultParseCart(database, cart, &pslFileName, &primerFileName, &target)) errAbort("PCR Result track has disappeared!"); char *fPrimer, *rPrimer; pcrResultGetPrimers(primerFileName, &fPrimer, &rPrimer); printf("<H2>PCR Results (<TT>%s %s</TT>)</H2>\n", fPrimer, rPrimer); printf("<B>Forward primer:</B> 5' <TT>%s</TT> 3'<BR>\n", fPrimer); printf("<B>Reverse primer:</B> 5' <TT>%s</TT> 3'<BR>\n", rPrimer); if (target != NULL) printf("<B>Search target:</B> %s<BR>\n", target->description); struct psl *itemPsl = NULL, *otherPsls = NULL, *psl; if (target != NULL) { /* item (from hgTracks) is |-separated: target sequence name, * amplicon start offset in target sequence, and amplicon end offset. */ char *words[3]; int wordCount = chopByChar(cloneString(item), '|', words, ArraySize(words)); if (wordCount != 3) errAbort("doPcrResult: expected 3 |-sep'd words but got '%s'", item); char *targetSeqName = words[0]; if (endsWith(targetSeqName, "__")) targetSeqName[strlen(targetSeqName)-2] = '\0'; int ampStart = atoi(words[1]), ampEnd = atoi(words[2]); pcrResultGetPsl(pslFileName, target, targetSeqName, seqName, ampStart, ampEnd, &itemPsl, &otherPsls); printPcrTargetMatch(target, itemPsl, TRUE); } else { pcrResultGetPsl(pslFileName, target, item, seqName, cartInt(cart, "o"), cartInt(cart, "t"), &itemPsl, &otherPsls); printPosOnChrom(itemPsl->tName, itemPsl->tStart, itemPsl->tEnd, itemPsl->strand, FALSE, NULL); } if (otherPsls != NULL) { puts("<HR>"); printf("<B>Other matches for these primers:</B><BR>\n"); for (psl = otherPsls; psl != NULL; psl = psl->next) { puts("<BR>"); if (target != NULL) printPcrTargetMatch(target, psl, FALSE); else printPosOnChrom(psl->tName, psl->tStart, psl->tEnd, psl->strand, FALSE, NULL); } puts("<HR>"); } printPcrSequence(target, itemPsl, fPrimer, rPrimer); puts("<BR><HR>"); printTrackHtml(tdb); } void doUserPsl(char *track, char *item) /* Process click on user-defined alignment. */ { int start = cartInt(cart, "o"); struct lineFile *lf; struct psl *pslList = NULL, *psl; char *pslName, *faName, *qName; enum gfType qt, tt; cartWebStart(cart, database, "BLAT Search Alignments"); printf("<H2>BLAT Search Alignments</H2>\n"); printf("<H3>Click on a line to see detailed letter-by-letter display</H3>"); parseSs(item, &pslName, &faName, &qName); pslxFileOpen(pslName, &qt, &tt, &lf); while ((psl = pslNext(lf)) != NULL) { if (sameString(psl->qName, qName)) { slAddHead(&pslList, psl); } else { pslFree(&psl); } } slSort(&pslList, pslCmpScore); lineFileClose(&lf); printAlignments(pslList, start, "htcUserAli", "user", item); pslFreeList(&pslList); webIncludeHelpFile(USER_PSL_TRACK_NAME, TRUE); } void doHgGold(struct trackDb *tdb, char *fragName) /* Click on a fragment of golden path. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); struct sqlConnection *conn3 = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char query2[256]; struct sqlResult *sr2; char **row2; char query3[256]; struct sqlResult *sr3; char **row3; struct agpFrag frag; struct contigAcc contigAcc; int start = cartInt(cart, "o"); boolean hasBin; char splitTable[HDB_MAX_TABLE_STRING]; char *chp; char *accession1, *accession2, *spanner, *variation, *varEvidence, *contact, *remark, *comment; // char *evaluation; unused variable char *secondAcc, *secondAccVer; char *tmpString; int first; cartWebStart(cart, database, "%s", fragName); if (!hFindSplitTable(database, seqName, tdb->table, splitTable, sizeof splitTable, &hasBin)) errAbort("doHgGold track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where frag = '%s' and chromStart = %d", splitTable, fragName, start); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); agpFragStaticLoad(row+hasBin, &frag); printf("<B>Entrez nucleotide:</B><A TARGET=_blank HREF='https://www.ncbi.nlm.nih.gov/nuccore/%s'> %s</A><BR>\n", fragName, fragName); printf("<B>Clone Fragment ID:</B> %s<BR>\n", frag.frag); printf("<B>Clone Fragment Type:</B> %s<BR>\n", frag.type); printf("<B>Clone Bases:</B> %d-%d<BR>\n", frag.fragStart+1, frag.fragEnd); if (hTableExists(database, "contigAcc")) { sqlSafef(query2, sizeof query2, "select * from contigAcc where contig = '%s'", frag.frag); if ((sr2 = sqlGetResult(conn2, query2))) { row = sqlNextRow(sr2); if (row) { contigAccStaticLoad(row, &contigAcc); printf("<B>Genbank Accession: <A HREF="); printEntrezNucleotideUrl(stdout, contigAcc.acc); printf(" TARGET=_BLANK>%s</A></B><BR>\n", contigAcc.acc); } sqlFreeResult(&sr2); } } printPos(frag.chrom, frag.chromStart, frag.chromEnd, frag.strand, FALSE, NULL); if (hTableExists(database, "certificate")) { first = 1; again: tmpString = cloneString(frag.frag); chp = strstr(tmpString, "."); if (chp != NULL) *chp = '\0'; if (first) { sqlSafef(query2, sizeof query2, "select * from certificate where accession1='%s';", tmpString); } else { sqlSafef(query2, sizeof query2, "select * from certificate where accession2='%s';", tmpString); } sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { printf("<HR>"); accession1 = row2[0]; accession2 = row2[1]; spanner = row2[2]; // evaluation = row2[3]; unused variable variation = row2[4]; varEvidence = row2[5]; contact = row2[6]; remark = row2[7]; comment = row2[8]; if (first) { secondAcc = accession2; } else { secondAcc = accession1; } sqlSafef(query3, sizeof query3, "select frag from %s where frag like '%s.%c';", splitTable, secondAcc, '%'); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); if (row3 != NULL) { secondAccVer = row3[0]; } else { secondAccVer = secondAcc; } printf("<H3>Non-standard Join Certificate: </H3>\n"); printf("The join between %s and %s is not standard due to a ", frag.frag, secondAccVer); printf("sub-optimal sequence alignment between the overlapping regions of the "); printf("clones. The following details are provided by the "); printf("sequencing center to support the joining of these two clones:<BR><BR>"); printf("<B>Joined with Fragment: </B> %s<BR>\n", secondAccVer); if (strcmp(spanner, "") != 0) printf("<B>Spanner: </B> %s<BR>\n", spanner); /* if (strcmp(evaluation, "") != 0) printf("<B>Evaluation: </B> %s<BR>\n", evaluation); */ if (strcmp(variation, "") != 0) printf("<B>Variation: </B> %s<BR>\n", variation); if (strcmp(varEvidence, "")!= 0) printf("<B>Variation Evidence: </B> %s<BR>\n", varEvidence); if (strcmp(remark, "") != 0) printf("<B>Remark: </B> %s<BR>\n", remark); if (strcmp(comment, "") != 0) printf("<B>Comment: </B> %s<BR>\n", comment); if (strcmp(contact, "") != 0) printf("<B>Contact: </B> <A HREF=\"mailto:%s\">%s</A><BR>", contact, contact); sqlFreeResult(&sr3); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); if (first) { first = 0; goto again; } } sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn2); hFreeConn(&conn3); printTrackHtml(tdb); } void doHgGap(struct trackDb *tdb, char *gapType) /* Print a teeny bit of info about a gap. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; struct agpGap gap; int start = cartInt(cart, "o"); boolean hasBin; char splitTable[HDB_MAX_TABLE_STRING]; cartWebStart(cart, database, "Gap in Sequence"); if (!hFindSplitTable(database, seqName, tdb->table, splitTable, sizeof splitTable, &hasBin)) errAbort("doHgGap track %s not found", tdb->table); if (sameString(tdb->table, splitTable)) sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart = %d", splitTable, seqName, start); else sqlSafef(query, sizeof(query), "select * from %s where chromStart = %d", splitTable, start); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) errAbort("Couldn't find gap at %s:%d", seqName, start); agpGapStaticLoad(row+hasBin, &gap); printf("<B>Gap Type:</B> %s<BR>\n", gap.type); printf("<B>Bridged:</B> %s<BR>\n", gap.bridge); printPos(gap.chrom, gap.chromStart, gap.chromEnd, NULL, FALSE, NULL); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void selectOneRow(struct sqlConnection *conn, char *table, char *query, struct sqlResult **retSr, char ***retRow) /* Do query and return one row offset by bin as needed. */ { char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin; char **row; if (!hFindSplitTable(database, seqName, table, fullTable, sizeof fullTable, &hasBin)) errAbort("Table %s doesn't exist in database", table); *retSr = sqlGetResult(conn, query); if ((row = sqlNextRow(*retSr)) == NULL) errAbort("No match to query '%s'", query); *retRow = row + hasBin; } void doHgContig(struct trackDb *tdb, char *ctgName) /* Click on a contig. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); char query[256], query2[256], ctgUrl[256]; struct sqlResult *sr, *sr2; char **row; struct ctgPos *ctg; struct ctgPos2 *ctg2 = NULL; int cloneCount; struct contigAcc contigAcc; char *ncbiTerm = cgiEncode(ctgName); safef(ctgUrl, sizeof(ctgUrl), "%s%s", NUCCORE_SEARCH, ncbiTerm); genericHeader(tdb, ctgName); char *url = tdb->url; if (sameWord(database,"oryCun2")) printf("<B>Name:</B> %s<BR>\n", ctgName); else if (isNotEmpty(url)) { if (sameWord(url, "none")) printf("<B>Name:</B> %s<BR>\n", ctgName); else printCustomUrl(tdb, ctgName, TRUE); } else printf("<B>Name:</B> <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", ctgUrl, ctgName); freeMem(ncbiTerm); sqlSafef(query, sizeof(query), "select * from %s where contig = '%s'", tdb->table, ctgName); selectOneRow(conn, tdb->table, query, &sr, &row); if (sameString("ctgPos2", tdb->table)) { ctg2 = ctgPos2Load(row); printf("<B>Type:</B> %s<BR>\n", ctg2->type); ctg = (struct ctgPos*)ctg2; } else ctg = ctgPosLoad(row); sqlFreeResult(&sr); if (hTableExists(database, "contigAcc")) { sqlSafef(query2, sizeof query2, "select * from contigAcc where contig = '%s'", ctgName); if ((sr2 = sqlGetResult(conn2, query2))) { row = sqlNextRow(sr2); if (row) { contigAccStaticLoad(row, &contigAcc); printf("<B>Genbank Accession: <A HREF="); printEntrezNucleotideUrl(stdout, contigAcc.acc); printf(" TARGET=_BLANK>%s</A></B><BR>\n", contigAcc.acc); } sqlFreeResult(&sr2); } } if (hTableExists(database, "clonePos")) { sqlSafef(query, sizeof query, "select count(*) from clonePos" " where chrom = '%s' and chromEnd >= %d and chromStart <= %d", ctg->chrom, ctg->chromStart, ctg->chromEnd); cloneCount = sqlQuickNum(conn, query); printf("<B>Total Clones:</B> %d<BR>\n", cloneCount); } printPos(ctg->chrom, ctg->chromStart, ctg->chromEnd, NULL, TRUE, ctg->contig); printTrackHtml(tdb); hFreeConn(&conn); hFreeConn(&conn2); } char *cloneStageName(char *stage) /* Expand P/D/F. */ { switch (stage[0]) { case 'P': return "predraft (less than 4x coverage shotgun)"; case 'D': return "draft (at least 4x coverage shotgun)"; case 'F': return "finished"; default: return "unknown"; } } void doHgCover(struct trackDb *tdb, char *cloneName) /* Respond to click on clone. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; struct clonePos *clone; int fragCount; cartWebStart(cart, database, "%s", cloneName); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, cloneName); selectOneRow(conn, tdb->table, query, &sr, &row); clone = clonePosLoad(row); sqlFreeResult(&sr); sqlSafef(query, sizeof query, "select count(*) from %s_gl where end >= %d and start <= %d and frag like '%s%%'", clone->chrom, clone->chromStart, clone->chromEnd, clone->name); fragCount = sqlQuickNum(conn, query); printf("<H2>Information on <A HREF=\""); printEntrezNucleotideUrl(stdout, cloneName); printf("\" TARGET=_blank>%s</A></H2>\n", cloneName); printf("<B>GenBank: <A HREF=\""); printEntrezNucleotideUrl(stdout, cloneName); printf("\" TARGET=_blank>%s</A></B> <BR>\n", cloneName); printf("<B>Status:</B> %s<BR>\n", cloneStageName(clone->stage)); printf("<B>Fragments:</B> %d<BR>\n", fragCount); printf("<B>Size:</B> %d bases<BR>\n", clone->seqSize); printf("<B>Chromosome:</B> %s<BR>\n", skipChr(clone->chrom)); printf("<BR>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void doHgClone(struct trackDb *tdb, char *fragName) /* Handle click on a clone. */ { char cloneName[128]; fragToCloneVerName(fragName, cloneName); doHgCover(tdb, cloneName); } void doBactigPos(struct trackDb *tdb, char *bactigName) /* Click on a bactig. */ { struct bactigPos *bactig; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char goldTable[16]; char ctgStartStr[16]; int ctgStart; genericHeader(tdb, bactigName); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, bactigName); selectOneRow(conn, tdb->table, query, &sr, &row); bactig = bactigPosLoad(row); sqlFreeResult(&sr); printf("<B>Name:</B> %s<BR>\n", bactigName); snprintf(goldTable, sizeof(goldTable), "%s_gold", seqName); puts("<B>First contig:</B>"); if (hTableExists(database, goldTable)) { sqlSafef(query, sizeof(query), "select chromStart from %s where frag = \"%s\"", goldTable, bactig->startContig); ctgStart = sqlQuickNum(conn, query); snprintf(ctgStartStr, sizeof(ctgStartStr), "%d", ctgStart); hgcAnchor("gold", bactig->startContig, ctgStartStr); } printf("%s</A><BR>\n", bactig->startContig); puts("<B>Last contig:</B>"); if (hTableExists(database, goldTable)) { sqlSafef(query, sizeof(query), "select chromStart from %s where frag = \"%s\"", goldTable, bactig->endContig); ctgStart = sqlQuickNum(conn, query); snprintf(ctgStartStr, sizeof(ctgStartStr), "%d", ctgStart); hgcAnchor("gold", bactig->endContig, ctgStartStr); } printf("%s</A><BR>\n", bactig->endContig); printPos(bactig->chrom, bactig->chromStart, bactig->chromEnd, NULL, FALSE,NULL); printTrackHtml(tdb); hFreeConn(&conn); } int showGfAlignment(struct psl *psl, bioSeq *qSeq, FILE *f, enum gfType qType, int qStart, int qEnd, char *qName) /* Show protein/DNA alignment or translated DNA alignment. */ { int blockCount; int tStart = psl->tStart; int tEnd = psl->tEnd; char tName[256]; struct dnaSeq *tSeq; /* protein psl's have a tEnd that isn't quite right */ if ((psl->strand[1] == '+') && (qType == gftProt)) tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1] * 3; tSeq = hDnaFromSeq(database, seqName, tStart, tEnd, dnaLower); freez(&tSeq->name); tSeq->name = cloneString(psl->tName); safef(tName, sizeof(tName), "%s.%s", organism, psl->tName); if (qName == NULL) fprintf(f, "<H2>Alignment of %s and %s:%d-%d</H2>\n", psl->qName, psl->tName, psl->tStart+1, psl->tEnd); else fprintf(f, "<H2>Alignment of %s and %s:%d-%d</H2>\n", qName, psl->tName, psl->tStart+1, psl->tEnd); fputs("Click on links in the frame to the left to navigate through " "the alignment.\n", f); blockCount = pslShowAlignment(psl, qType == gftProt, qName, qSeq, qStart, qEnd, tName, tSeq, tStart, tEnd, f); freeDnaSeq(&tSeq); return blockCount; } struct ffAli *pslToFfAliAndSequence(struct psl *psl, struct dnaSeq *qSeq, boolean *retIsRc, struct dnaSeq **retSeq, int *retTStart) /* Given psl, dig up target sequence and convert to ffAli. * Note: if strand is -, this does a pslRc to psl! */ { int tStart, tEnd, tRcAdjustedStart; struct dnaSeq *dnaSeq; tStart = psl->tStart - 100; if (tStart < 0) tStart = 0; if (retTStart) *retTStart = tStart; tEnd = psl->tEnd + 100; if (tEnd > psl->tSize) tEnd = psl->tSize; dnaSeq = hDnaFromSeq(database, seqName, tStart, tEnd, dnaLower); freez(&dnaSeq->name); dnaSeq->name = cloneString(psl->tName); if (retSeq) *retSeq = dnaSeq; tRcAdjustedStart = tStart; if (psl->strand[1] == '-') pslRc(psl); if (psl->strand[0] == '-') { if (retIsRc) *retIsRc = TRUE; reverseComplement(dnaSeq->dna, dnaSeq->size); pslRc(psl); tRcAdjustedStart = psl->tSize - tEnd; } return pslToFfAli(psl, qSeq, dnaSeq, tRcAdjustedStart); } int showPartialDnaAlignment(struct psl *wholePsl, struct dnaSeq *rnaSeq, FILE *body, int cdsS, int cdsE, boolean restrictToWindow) /* Show (part of) alignment for accession. wholePsl is the whole alignment; * if restrictToWindow then display the part of the alignment in the current * browser window. */ { struct dnaSeq *dnaSeq; int wholeTStart; int partTStart = wholePsl->tStart, partTEnd = wholePsl->tEnd; DNA *rna; int rnaSize; boolean isRc = FALSE; struct ffAli *wholeFfAli; int blockCount; /* Get RNA sequence and convert psl to ffAli. */ rna = rnaSeq->dna; rnaSize = rnaSeq->size; /* Don't forget -- this may change wholePsl! */ wholeFfAli = pslToFfAliAndSequence(wholePsl, rnaSeq, &isRc, &dnaSeq, &wholeTStart); if (restrictToWindow) { partTStart = max(wholePsl->tStart, winStart); partTEnd = min(wholePsl->tEnd, winEnd); } /* Write body heading info. */ fprintf(body, "<H2>Alignment of %s and %s:%d-%d</H2>\n", wholePsl->qName, wholePsl->tName, partTStart+1, partTEnd); fprintf(body, "Click on links in the frame to the left to navigate through " "the alignment.\n"); if (rnaSize != wholePsl->qSize) { fprintf(body, "<p><b>Cannot display alignment. Size of rna %s is %d has changed since alignment was performed when it was %d.\n", wholePsl->qName, rnaSize, wholePsl->qSize); return 0; } blockCount = ffShAliPart(body, wholeFfAli, wholePsl->qName, rna, rnaSize, 0, dnaSeq->name, dnaSeq->dna, dnaSeq->size, wholeTStart, 8, FALSE, isRc, FALSE, TRUE, TRUE, TRUE, TRUE, cdsS, cdsE, partTStart, partTEnd); return blockCount; } void showSomeAlignment(struct psl *psl, bioSeq *oSeq, enum gfType qType, int qStart, int qEnd, char *qName, int cdsS, int cdsE) /* Display protein or DNA alignment in a frame. */ { int blockCount, i; struct tempName indexTn, bodyTn; FILE *index, *body; trashDirFile(&indexTn, "index", "index", ".html"); trashDirFile(&bodyTn, "body", "body", ".html"); /* Writing body of alignment. */ body = mustOpen(bodyTn.forCgi, "w"); htmStartDirDepth(body, psl->qName, 2); if (qType == gftRna || qType == gftDna) blockCount = showPartialDnaAlignment(psl, oSeq, body, cdsS, cdsE, FALSE); else blockCount = showGfAlignment(psl, oSeq, body, qType, qStart, qEnd, qName); htmEnd(body); fclose(body); chmod(bodyTn.forCgi, 0666); /* Write index. */ index = mustOpen(indexTn.forCgi, "w"); if (qName == NULL) qName = psl->qName; htmStartDirDepth(index, qName, 2); fprintf(index, "<H3>Alignment of %s</H3>", qName); fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, qName); fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), psl->tName); for (i=1; i<=blockCount; ++i) { fprintf(index, "<A HREF=\"../%s#%d\" TARGET=\"body\">block%d</A><BR>\n", bodyTn.forCgi, i, i); } fprintf(index, "<A HREF=\"../%s#ali\" TARGET=\"body\">together</A><BR>\n", bodyTn.forCgi); htmEnd(index); fclose(index); chmod(indexTn.forCgi, 0666); /* Write (to stdout) the main html page containing just the frame info. */ puts("<FRAMESET COLS = \"13%,87% \" >"); printf(" <FRAME SRC=\"%s\" NAME=\"index\">\n", indexTn.forCgi); printf(" <FRAME SRC=\"%s\" NAME=\"body\">\n", bodyTn.forCgi); puts("<NOFRAMES><BODY></BODY></NOFRAMES>"); puts("</FRAMESET>"); puts("</HTML>\n"); exit(0); /* Avoid cartHtmlEnd. */ } void showSomePartialDnaAlignment(struct psl *partPsl, struct psl *wholePsl, bioSeq *oSeq, char *qName, int cdsS, int cdsE) /* Display protein or DNA alignment in a frame. */ { int blockCount, i; struct tempName indexTn, bodyTn; FILE *index, *body; trashDirFile(&indexTn, "index", "index", ".html"); trashDirFile(&bodyTn, "body", "body", ".html"); /* Writing body of alignment. */ body = mustOpen(bodyTn.forCgi, "w"); htmStartDirDepth(body, partPsl->qName, 2); blockCount = showPartialDnaAlignment(wholePsl, oSeq, body, cdsS, cdsE, TRUE); htmEnd(body); fclose(body); chmod(bodyTn.forCgi, 0666); /* Write index. */ index = mustOpen(indexTn.forCgi, "w"); if (qName == NULL) qName = partPsl->qName; htmStartDirDepth(index, qName, 2); fprintf(index, "<H3>Alignment of %s</H3>", qName); fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, qName); if (partPsl != wholePsl) fprintf(index, "<A HREF=\"../%s#cDNAStart\" TARGET=\"body\">%s in browser window</A><BR>\n", bodyTn.forCgi, qName); fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), partPsl->tName); for (i=1; i<=blockCount; ++i) { fprintf(index, "<A HREF=\"../%s#%d\" TARGET=\"body\">block%d</A><BR>\n", bodyTn.forCgi, i, i); } fprintf(index, "<A HREF=\"../%s#ali\" TARGET=\"body\">together</A><BR>\n", bodyTn.forCgi); htmEnd(index); fclose(index); chmod(indexTn.forCgi, 0666); /* Write (to stdout) the main html page containing just the frame info. */ if (partPsl != wholePsl) printf("<FRAMESET COLS = \"13%%,87%% \" " "ONLOAD=\"body.location.href = '%s#cDNAStart';\">\n", bodyTn.forCgi); else puts("<FRAMESET COLS = \"13%,87% \" >"); printf(" <FRAME SRC=\"%s\" NAME=\"index\">\n", indexTn.forCgi); printf(" <FRAME SRC=\"%s\" NAME=\"body\">\n", bodyTn.forCgi); puts("<NOFRAMES><BODY></BODY></NOFRAMES>"); puts("</FRAMESET>"); puts("</HTML>\n"); exit(0); /* Avoid cartHtmlEnd. */ } static void getCdsStartAndStop(struct sqlConnection *conn, char *acc, char *trackTable, uint *retCdsStart, uint *retCdsEnd) /* Get cds start and stop, if available */ { struct trackDb *tdb = hashFindVal(trackHash, trackTable); // Note: this variable was previously named cdsTable but unfortunately the // hg/(inc|lib)/genbank.[hc] code uses the global var cdsTable! char *tdbCdsTable = tdb ? trackDbSetting(tdb, "cdsTable") : NULL; if (isEmpty(tdbCdsTable) && startsWith("ncbiRefSeq", trackTable)) tdbCdsTable = "ncbiRefSeqCds"; if (isNotEmpty(tdbCdsTable) && hTableExists(database, tdbCdsTable)) { char query[256]; sqlSafef(query, sizeof(query), "select cds from %s where id = '%s'", tdbCdsTable, acc); char *cdsString = sqlQuickString(conn, query); if (isNotEmpty(cdsString)) genbankParseCds(cdsString, retCdsStart, retCdsEnd); } else if (sqlTableExists(conn, gbCdnaInfoTable)) { char accChopped[512]; safecpy(accChopped, sizeof(accChopped), acc); chopSuffix(accChopped); char query[256]; sqlSafef(query, sizeof query, "select cds from %s where acc = '%s'", gbCdnaInfoTable, accChopped); char *cdsId = sqlQuickString(conn, query); if (isNotEmpty(cdsId)) { sqlSafef(query, sizeof query, "select name from %s where id = '%s'", cdsTable, cdsId); char *cdsString = sqlQuickString(conn, query); if (isNotEmpty(cdsString)) genbankParseCds(cdsString, retCdsStart, retCdsEnd); } } } void htcBigPslAli(char *acc) /* Show alignment for accession in bigPsl file. */ { struct psl *psl; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; aliTable = cartString(cart, "aliTable"); if (isCustomTrack(aliTable)) { struct customTrack *ct = lookupCt(aliTable); tdb = ct->tdb; } else tdb = hashFindVal(trackHash, aliTable); char title[1024]; safef(title, sizeof title, "%s vs Genomic [%s]", acc, aliTable); htmlFramesetStart(title); /* Get some environment vars. */ start = cartInt(cart, "l"); int end = cartInt(cart, "r"); char *chrom = cartString(cart, "c"); char *seq, *cdsString = NULL; struct lm *lm = lmInit(0); char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table); struct bbiFile *bbi = bigBedFileOpen(fileName); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, seqName, startBuf, endBuf, bedRow, ArraySize(bedRow)); struct bed *bed = bedLoadN(bedRow, 12); if (sameString(bed->name, acc) && (bb->start == start) && (bb->end == end)) { bb->next = NULL; break; } } if (bb == NULL) errAbort("item %s not found in range %s:%d-%d in bigBed %s (%s)", acc, chrom, start, end, tdb->table, fileName); unsigned seqTypeField = bbExtraFieldIndex(bbi, "seqType"); psl = pslFromBigPsl(seqName, bb, seqTypeField, &seq, &cdsString); if (cdsString) genbankParseCds(cdsString, &cdsStart, &cdsEnd); if (seq == NULL) { printf("Sequence for %s not available.\n", psl->qName); return; } struct dnaSeq *rnaSeq = newDnaSeq(seq, strlen(seq), acc); enum gfType type = gftRna; if (pslIsProtein(psl)) type = gftProt; showSomeAlignment(psl, rnaSeq, type, 0, rnaSeq->size, NULL, cdsStart, cdsEnd); } void htcBigPslAliInWindow(char *acc) /* Show alignment in window for accession in bigPsl file. */ { struct psl *partPsl, *wholePsl; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; aliTable = cartString(cart, "aliTable"); if (isCustomTrack(aliTable)) { struct customTrack *ct = lookupCt(aliTable); tdb = ct->tdb; } else tdb = hashFindVal(trackHash, aliTable); char title[1024]; safef(title, sizeof title, "%s vs Genomic [%s]", acc, aliTable); htmlFramesetStart(title); /* Get some environment vars. */ start = cartInt(cart, "l"); int end = cartInt(cart, "r"); char *chrom = cartString(cart, "c"); char *seq, *cdsString = NULL; struct lm *lm = lmInit(0); char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table); struct bbiFile *bbi = bigBedFileOpen(fileName); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, seqName, startBuf, endBuf, bedRow, ArraySize(bedRow)); struct bed *bed = bedLoadN(bedRow, 12); if (sameString(bed->name, acc)) { bb->next = NULL; break; } } unsigned seqTypeField = bbExtraFieldIndex(bbi, "seqType"); wholePsl = pslFromBigPsl(seqName, bb, seqTypeField, &seq, &cdsString); if (seq == NULL) { printf("Sequence for %s not available.\n", wholePsl->qName); return; } if (cdsString) genbankParseCds(cdsString, &cdsStart, &cdsEnd); if (wholePsl->tStart >= winStart && wholePsl->tEnd <= winEnd) partPsl = wholePsl; else partPsl = pslTrimToTargetRange(wholePsl, winStart, winEnd); struct dnaSeq *rnaSeq = newDnaSeq(seq, strlen(seq), acc); showSomePartialDnaAlignment(partPsl, wholePsl, rnaSeq, NULL, cdsStart, cdsEnd); } static struct dnaSeq *getBaseColorSequence(char *itemName, char *table) /* Grab sequence using the sequence and extFile table names out of BASE_COLOR_USE_SEQUENCE. */ { struct trackDb *tdb = hashMustFindVal(trackHash, table); char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE); char *specCopy = cloneString(spec); // value is: extFile seqTbl extFileTbl // or: db [dddBbb1] char *words[3]; int nwords = chopByWhite(specCopy, words, ArraySize(words)); if (sameString(words[0], "extFile") && (nwords == ArraySize(words))) return hDnaSeqGet(database, itemName, words[1], words[2]); else if (sameString(words[0], "db")) { char *db = (nwords == 2) ? words[1] : database; return hChromSeq(db, itemName, 0, 0); } else errAbort("invalid %s track setting: %s", BASE_COLOR_USE_SEQUENCE, spec); return NULL; // make compiler happy } void htcCdnaAli(char *acc) /* Show alignment for accession. */ { char query[256]; char table[HDB_MAX_TABLE_STRING]; char accTmp[64]; struct sqlConnection *conn; struct sqlResult *sr; char **row; struct psl *psl; struct dnaSeq *rnaSeq; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; boolean hasBin; char accChopped[512] ; safef(accChopped, sizeof(accChopped), "%s",acc); chopSuffix(accChopped); aliTable = cartString(cart, "aliTable"); char *accForTitle = startsWith("ncbiRefSeq", aliTable) ? acc : accChopped; char title[1024]; safef(title, sizeof title, "%s vs Genomic [%s]", accForTitle, aliTable); htmlFramesetStart(title); /* Get some environment vars. */ start = cartInt(cart, "o"); conn = hAllocConn(database); getCdsStartAndStop(conn, acc, aliTable, &cdsStart, &cdsEnd); /* Look up alignments in database */ if (!hFindSplitTable(database, seqName, aliTable, table, sizeof table, &hasBin)) errAbort("Failed to find aliTable=%s", aliTable); sqlSafef(query, sizeof query, "select * from %s where qName like '%s%%' and tName=\"%s\" and tStart=%d", table, acc, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", acc, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); /* get bz rna snapshot for blastz alignments */ if (sameString("mrnaBlastz", aliTable) || sameString("pseudoMrna", aliTable)) { struct sqlConnection *conn = hAllocConn(database); unsigned retId = 0; safef(accTmp, sizeof accTmp, "bz-%s", acc); if (hRnaSeqAndIdx(accTmp, &rnaSeq, &retId, conn) == -1) rnaSeq = hRnaSeq(database, acc); hFreeConn(&conn); } else if (sameString("HInvGeneMrna", aliTable)) { /* get RNA accession for the gene id in the alignment */ sqlSafef(query, sizeof query, "select mrnaAcc from HInv where geneId='%s'", acc); rnaSeq = hRnaSeq(database, sqlQuickString(conn, query)); } else if (sameString("ncbiRefSeqPsl", aliTable) || startsWith("altSeqLiftOverPsl", aliTable) || startsWith("fixSeqLiftOverPsl", aliTable)) { rnaSeq = getBaseColorSequence(acc, aliTable); } else { char *cdnaTable = NULL; struct trackDb *tdb = hashFindVal(trackHash, aliTable); if (tdb != NULL) cdnaTable = trackDbSetting(tdb, "cdnaTable"); if (isNotEmpty(cdnaTable) && hTableExists(database, cdnaTable)) rnaSeq = hGenBankGetMrna(database, acc, cdnaTable); else rnaSeq = hRnaSeq(database, acc); } if (NULL == rnaSeq) { printf("RNA sequence not found: '%s'", acc); } else { if (startsWith("xeno", aliTable)) showSomeAlignment(psl, rnaSeq, gftDnaX, 0, rnaSeq->size, NULL, cdsStart, cdsEnd); else showSomeAlignment(psl, rnaSeq, gftDna, 0, rnaSeq->size, NULL, cdsStart, cdsEnd); } hFreeConn(&conn); } void htcCdnaAliInWindow(char *acc) /* Show part of alignment in browser window for accession. */ { char query[256]; char table[64]; struct sqlConnection *conn; struct sqlResult *sr; char **row; struct psl *wholePsl, *partPsl; struct dnaSeq *rnaSeq; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; boolean hasBin; char accChopped[512] ; safef(accChopped, sizeof(accChopped), "%s",acc); chopSuffix(accChopped); /* Get some environment vars. */ aliTable = cartString(cart, "aliTable"); start = cartInt(cart, "o"); char *accForTitle = startsWith("ncbiRefSeq", aliTable) ? acc : accChopped; char title[1024]; safef(title, sizeof title, "%s vs Genomic [%s]", accForTitle, aliTable); htmlFramesetStart(title); conn = hAllocConn(database); getCdsStartAndStop(conn, acc, aliTable, &cdsStart, &cdsEnd); if (startsWith("user", aliTable)) { char *pslName, *faName, *qName; struct lineFile *lf; bioSeq *oSeqList = NULL, *oSeq = NULL; struct psl *psl; int start; enum gfType tt, qt; boolean isProt; char *ss = cartOptionalString(cart, "ss"); if ((ss != NULL) && !ssFilesExist(ss)) { ss = NULL; cartRemove(cart, "ss"); errAbort("hgBlat temporary files not found"); } start = cartInt(cart, "o"); // itemIn is three words, the first two are the ss files and the third is the accession char *itemIn = cloneString(acc); char *words[3]; int numWords = chopByWhite(itemIn, words, 3); if (numWords != 3) errAbort("ItemIn string doesn't have three words."); qName = words[2]; parseSs(ss, &pslName, &faName, NULL); pslxFileOpen(pslName, &qt, &tt, &lf); isProt = (qt == gftProt); if (isProt) errAbort("hgBlat protein alignments not supported for htcCdnaAliInWindow"); while ((psl = pslNext(lf)) != NULL) { if (sameString(psl->tName, seqName) && sameString(psl->qName, qName) && psl->tStart == start ) break; pslFree(&psl); } lineFileClose(&lf); if (psl == NULL) errAbort("Couldn't find alignment at %s:%d", seqName, start); oSeqList = faReadAllSeq(faName, !isProt); for (oSeq = oSeqList; oSeq != NULL; oSeq = oSeq->next) { if (sameString(oSeq->name, qName)) break; } if (oSeq == NULL) errAbort("%s is in %s but not in %s. Internal error.", qName, pslName, faName); wholePsl = psl; rnaSeq = oSeq; } else { /* Look up alignments in database */ if (!hFindSplitTable(database, seqName, aliTable, table, sizeof table, &hasBin)) errAbort("aliTable %s not found", aliTable); sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName=\"%s\" and tStart=%d", table, acc, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", acc, start); wholePsl = pslLoad(row+hasBin); sqlFreeResult(&sr); if (startsWith("ucscRetroAli", aliTable) || startsWith("retroMrnaAli", aliTable) || sameString("pseudoMrna", aliTable) || startsWith("altSeqLiftOverPsl", aliTable) || startsWith("fixSeqLiftOverPsl", aliTable) || startsWith("ncbiRefSeqPsl", aliTable)) { rnaSeq = getBaseColorSequence(acc, aliTable); } else if (sameString("HInvGeneMrna", aliTable)) { /* get RNA accession for the gene id in the alignment */ sqlSafef(query, sizeof(query), "select mrnaAcc from HInv where geneId='%s'", acc); rnaSeq = hRnaSeq(database, sqlQuickString(conn, query)); } else { char *cdnaTable = NULL; struct trackDb *tdb = hashFindVal(trackHash, aliTable); if (tdb != NULL) cdnaTable = trackDbSetting(tdb, "cdnaTable"); if (isNotEmpty(cdnaTable) && hTableExists(database, cdnaTable)) rnaSeq = hGenBankGetMrna(database, acc, cdnaTable); else rnaSeq = hRnaSeq(database, acc); } } /* Get partial psl for part of alignment in browser window: */ if (wholePsl->tStart >= winStart && wholePsl->tEnd <= winEnd) partPsl = wholePsl; else partPsl = pslTrimToTargetRange(wholePsl, winStart, winEnd); if (startsWith("xeno", aliTable)) errAbort("htcCdnaAliInWindow does not support translated alignments."); else showSomePartialDnaAlignment(partPsl, wholePsl, rnaSeq, NULL, cdsStart, cdsEnd); hFreeConn(&conn); } void htcChainAli(char *item) /* Draw detailed alignment representation of a chain. */ { struct chain *chain; struct psl *fatPsl, *psl = NULL; int id = atoi(item); char *track = cartString(cart, "o"); char *type = trackTypeInfo(track); char *typeWords[2]; char *otherDb = NULL, *org = NULL, *otherOrg = NULL; struct dnaSeq *qSeq = NULL; char name[128]; /* Figure out other database. */ if (chopLine(type, typeWords) < ArraySize(typeWords)) errAbort("type line for %s is short in trackDb", track); otherDb = typeWords[1]; if (! sameWord(otherDb, "seq")) { otherOrg = hOrganism(otherDb); } org = hOrganism(database); /* Load up subset of chain and convert it to part of psl * that just fits inside of window. */ chain = chainLoadIdRange(database, track, seqName, winStart, winEnd, id); if (chain->blockList == NULL) { printf("None of chain is actually in the window"); return; } fatPsl = chainToPsl(chain); chainFree(&chain); psl = pslTrimToTargetRange(fatPsl, winStart, winEnd); pslFree(&fatPsl); if (sameWord(otherDb, "seq")) { qSeq = hExtSeqPart(database, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s", psl->qName); } else { qSeq = loadGenomePart(otherDb, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s.%s", otherOrg, psl->qName); } char title[1024]; safef(title, sizeof title, "%s %s vs %s %s ", (otherOrg == NULL ? "" : otherOrg), psl->qName, org, psl->tName ); htmlFramesetStart(title); showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, 0, 0); } void htcChainTransAli(char *item) /* Draw detailed alignment representation of a chain with translated protein */ { struct chain *chain; struct psl *fatPsl, *psl = NULL; int id = atoi(item); char *track = cartString(cart, "o"); char *type = trackTypeInfo(track); char *typeWords[2]; char *otherDb = NULL, *org = NULL, *otherOrg = NULL; struct dnaSeq *qSeq = NULL; char name[128]; int cdsStart = cgiInt("qs"); int cdsEnd = cgiInt("qe"); /* Figure out other database. */ if (chopLine(type, typeWords) < ArraySize(typeWords)) errAbort("type line for %s is short in trackDb", track); otherDb = typeWords[1]; if (! sameWord(otherDb, "seq")) { otherOrg = hOrganism(otherDb); } org = hOrganism(database); /* Load up subset of chain and convert it to part of psl * that just fits inside of window. */ chain = chainLoadIdRange(database, track, seqName, winStart, winEnd, id); if (chain->blockList == NULL) { printf("None of chain is actually in the window"); return; } fatPsl = chainToPsl(chain); chainFree(&chain); psl = pslTrimToTargetRange(fatPsl, winStart, winEnd); pslFree(&fatPsl); if (sameWord(otherDb, "seq")) { qSeq = hExtSeq(database, psl->qName); safef(name, sizeof name, "%s", psl->qName); } else { qSeq = loadGenomePart(otherDb, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s.%s", otherOrg, psl->qName); } char title[1024]; safef(title, sizeof title, "%s %s vs %s %s ", (otherOrg == NULL ? "" : otherOrg), psl->qName, org, psl->tName ); htmlFramesetStart(title); /*showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, 0, 0); */ showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, cdsStart, cdsEnd); } void htcUserAli(char *fileNames) /* Show alignment for accession. */ { char *pslName, *faName, *qName; struct lineFile *lf; bioSeq *oSeqList = NULL, *oSeq = NULL; struct psl *psl; int start; enum gfType tt, qt; boolean isProt; char title[1024]; safef(title, sizeof title, "User Sequence vs Genomic"); htmlFramesetStart(title); start = cartInt(cart, "o"); parseSs(fileNames, &pslName, &faName, &qName); pslxFileOpen(pslName, &qt, &tt, &lf); isProt = (qt == gftProt); while ((psl = pslNext(lf)) != NULL) { if (sameString(psl->tName, seqName) && psl->tStart == start && sameString(psl->qName, qName)) break; pslFree(&psl); } lineFileClose(&lf); if (psl == NULL) errAbort("Couldn't find alignment at %s:%d", seqName, start); oSeqList = faReadAllSeq(faName, !isProt); for (oSeq = oSeqList; oSeq != NULL; oSeq = oSeq->next) { if (sameString(oSeq->name, qName)) break; } if (oSeq == NULL) errAbort("%s is in %s but not in %s. Internal error.", qName, pslName, faName); showSomeAlignment(psl, oSeq, qt, 0, oSeq->size, NULL, 0, 0); } void htcProteinAli(char *readName, char *table) /* Show protein to translated dna alignment for accession. */ { struct psl *psl; int start; enum gfType qt = gftProt; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *seq = NULL; char query[256], **row; char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin; char buffer[256]; int addp = 0; char *pred = NULL; char title[1024]; safef(title, sizeof title, "Protein Sequence vs Genomic"); htmlFramesetStart(title); addp = cartUsualInt(cart, "addp",0); pred = cartUsualString(cart, "pred",NULL); start = cartInt(cart, "o"); if (!hFindSplitTable(database, seqName, table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", table); sqlSafef(query, sizeof query, "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", fullTable, readName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", readName, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); if ((addp == 1) || (pred != NULL)) { char *ptr; safef(buffer, sizeof buffer, "%s",readName); if (!(sameString(pred, "ce3.blastWBPep01") || sameString(pred, "ce9.blastSGPep01") || sameString(pred, "ce6.blastSGPep01") || sameString(pred, "ce4.blastSGPep01")) && (ptr = strchr(buffer, '.')) != NULL) { *ptr = 0; psl->qName = cloneString(buffer); *ptr++ = 'p'; *ptr = 0; } if (addp == 1) seq = hPepSeq(database, buffer); else { sqlSafef(query, sizeof(query), "select seq from %s where name = '%s'", pred, psl->qName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) seq = newDnaSeq(cloneString(row[0]), strlen(row[0]), psl->qName); else errAbort("Cannot find sequence for '%s' in %s",psl->qName, pred); sqlFreeResult(&sr); } } else seq = hPepSeq(database, readName); hFreeConn(&conn); showSomeAlignment(psl, seq, qt, 0, seq->size, NULL, 0, 0); } void htcBlatXeno(char *readName, char *table) /* Show alignment for accession. */ { struct psl *psl; int start; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *seq; char query[256], **row; char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin; char title[1024]; safef(title, sizeof title, "Sequence %s", readName); htmlFramesetStart(title); start = cartInt(cart, "o"); if (!hFindSplitTable(database, seqName, table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", table); sqlSafef(query, sizeof query, "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", fullTable, readName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", readName, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); hFreeConn(&conn); seq = hExtSeq(database, readName); showSomeAlignment(psl, seq, gftDnaX, 0, seq->size, NULL, 0, 0); } void writeMatches(FILE *f, char *a, char *b, int count) /* Write a | where a and b agree, a ' ' elsewhere. */ { int i; for (i=0; i<count; ++i) { if (a[i] == b[i]) fputc('|', f); else fputc(' ', f); } } void fetchAndShowWaba(char *table, char *name) /* Fetch and display waba alignment. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); struct wabAli *wa = NULL; int qOffset; char strand = '+'; sqlSafef(query, sizeof query, "select * from %s where query = '%s' and chrom = '%s' and chromStart = %d", table, name, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Sorry, couldn't find alignment of %s at %d of %s in database", name, start, seqName); wa = wabAliLoad(row); printf("<PRE><TT>"); qOffset = wa->qStart; if (wa->strand[0] == '-') { strand = '-'; qOffset = wa->qEnd; } xenShowAli(wa->qSym, wa->tSym, wa->hSym, wa->symCount, stdout, qOffset, wa->chromStart, strand, '+', 60); printf("</TT></PRE>"); wabAliFree(&wa); hFreeConn(&conn); } void doHgTet(struct trackDb *tdb, char *name) /* Do thing with tet track. */ { cartWebStart(cart, database, "Fish Alignment"); printf("Alignment between fish sequence %s (above) and human chromosome %s (below)\n", name, skipChr(seqName)); fetchAndShowWaba("waba_tet", name); } void doHgCbr(struct trackDb *tdb, char *name) /* Do thing with cbr track. */ { cartWebStart(cart, database, "Worm Alignment"); printf("Alignment between C briggsae sequence %s (above) and C elegans chromosome %s (below)\n", name, skipChr(seqName)); fetchAndShowWaba("wabaCbr", name); } void doHgRepeat(struct trackDb *tdb, char *repeat) /* Do click on a repeat track. */ { int offset = cartInt(cart, "o"); cartWebStart(cart, database, "Repeat"); if (offset >= 0) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct rmskOut *ro; char query[256]; char table[HDB_MAX_TABLE_STRING]; boolean hasBin; int start = cartInt(cart, "o"); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("Track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where repName = '%s' and genoName = '%s' and genoStart = %d", table, repeat, seqName, start); sr = sqlGetResult(conn, query); if (sameString(tdb->table,"rmskNew")) printf("<H3>CENSOR Information</H3>\n"); else printf("<H3>RepeatMasker Information</H3>\n"); while ((row = sqlNextRow(sr)) != NULL) { ro = rmskOutLoad(row+hasBin); printf("<B>Name:</B> <A HREF='http://www.girinst.org/protected/repbase_extract.php?access=%s'>%s</A>\n", ro->repName, ro->repName); printf("(link requires <A HREF='http://www.girinst.org/accountservices/register.php'>registration</A>)<BR>"); printf("<B>Family:</B> %s<BR>\n", ro->repFamily); printf("<B>Class:</B> %s<BR>\n", ro->repClass); printf("<B>SW Score:</B> %d<BR>\n", ro->swScore); printf("<B>Divergence:</B> %3.1f%%<BR>\n", 0.1 * ro->milliDiv); printf("<B>Deletions:</B> %3.1f%%<BR>\n", 0.1 * ro->milliDel); printf("<B>Insertions:</B> %3.1f%%<BR>\n", 0.1 * ro->milliIns); printf("<B>Begin in repeat:</B> %d<BR>\n", (ro->strand[0] == '-' ? ro->repLeft : ro->repStart)); printf("<B>End in repeat:</B> %d<BR>\n", ro->repEnd); printf("<B>Left in repeat:</B> %d<BR>\n", (ro->strand[0] == '-' ? -ro->repStart : -ro->repLeft)); printPos(seqName, ro->genoStart, ro->genoEnd, ro->strand, TRUE, ro->repName); } hFreeConn(&conn); } else { if (sameString(repeat, "SINE")) printf("This track contains the short interspersed nuclear element (SINE) class of repeats, which includes ALUs.\n"); else if (sameString(repeat, "LINE")) printf("This track contains the long interspersed nuclear element (LINE) class of repeats.\n"); else if (sameString(repeat, "LTR")) printf("This track contains the class of long terminal repeats (LTRs), which includes retroposons.\n"); else printf("This track contains the %s class of repeats.\n", repeat); printf("Click on an individual repeat element within the track for more information about that item.<BR>\n"); } printTrackHtml(tdb); } void doHgIsochore(struct trackDb *tdb, char *item) /* do click on isochore track. */ { cartWebStart(cart, database, "Isochore Info"); printf("<H2>Isochore Information</H2>\n"); if (cgiVarExists("o")) { struct isochores *iso; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { iso = isochoresLoad(row); printf("<B>Type:</B> %s<BR>\n", iso->name); printf("<B>GC Content:</B> %3.1f%%<BR>\n", 0.1*iso->gcPpt); printf("<B>Chromosome:</B> %s<BR>\n", skipChr(iso->chrom)); printf("<B>Begin in chromosome:</B> %d<BR>\n", iso->chromStart); printf("<B>End in chromosome:</B> %d<BR>\n", iso->chromEnd); printf("<B>Size:</B> %d<BR>\n", iso->chromEnd - iso->chromStart); printf("<BR>\n"); isochoresFree(&iso); } hFreeConn(&conn); } printTrackHtml(tdb); } void doSimpleRepeat(struct trackDb *tdb, char *item) /* Print info on simple repeat. */ { cartWebStart(cart, database, "Simple Repeat Info"); printf("<H2>Simple Tandem Repeat Information</H2>\n"); if (cgiVarExists("o")) { struct simpleRepeat *rep; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); int rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { rep = simpleRepeatLoad(row+rowOffset); printf("<B>Period:</B> %d<BR>\n", rep->period); printf("<B>Copies:</B> %4.1f<BR>\n", rep->copyNum); printf("<B>Consensus size:</B> %d<BR>\n", rep->consensusSize); printf("<B>Match Percentage:</B> %d%%<BR>\n", rep->perMatch); printf("<B>Insert/Delete Percentage:</B> %d%%<BR>\n", rep->perIndel); printf("<B>Score:</B> %d<BR>\n", rep->score); printf("<B>Entropy:</B> %4.3f<BR>\n", rep->entropy); printf("<B>Sequence:</B> %s<BR>\n", rep->sequence); printPos(seqName, rep->chromStart, rep->chromEnd, NULL, TRUE, rep->name); printf("<BR>\n"); simpleRepeatFree(&rep); } hFreeConn(&conn); } else { puts("<P>Click directly on a repeat for specific information on that repeat</P>"); } printTrackHtml(tdb); } void hgSoftPromoter(char *track, char *item) /* Print info on Softberry promoter. */ { cartWebStart(cart, database, "Softberry TSSW Promoter"); printf("<H2>Softberry TSSW Promoter Prediction %s</H2>", item); if (cgiVarExists("o")) { struct softPromoter *pro; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); int rowOffset = hOffsetPastBin(database, seqName, track); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", track, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { pro = softPromoterLoad(row+rowOffset); bedPrintPos((struct bed *)pro, 3, NULL); printf("<B>Short Name:</B> %s<BR>\n", pro->name); printf("<B>Full Name:</B> %s<BR>\n", pro->origName); printf("<B>Type:</B> %s<BR>\n", pro->type); printf("<B>Score:</B> %f<BR>\n", pro->origScore); printf("<B>Block Info:</B> %s<BR>\n", pro->blockString); printf("<BR>\n"); htmlHorizontalLine(); printCappedSequence(pro->chromStart, pro->chromEnd, 100); softPromoterFree(&pro); htmlHorizontalLine(); } hFreeConn(&conn); } printf("<P>This track was kindly provided by Victor Solovyev (EOS Biotechnology Inc.) on behalf of "); printf("<A HREF=\"http://www.softberry.com\" TARGET=_blank>Softberry Inc.</A> "); puts("using the TSSW program. " "Commercial use of these predictions is restricted to viewing in " "this browser. Please contact Softberry Inc. to make arrangements " "for further commercial access. Further information from Softberry on" "this track appears below.</P>" "<P>\"Promoters were predicted by Softberry promoter prediction program TSSW in " "regions up to 3000 from known starts of coding regions (ATG codon) or known " "mapped 5'-mRNA ends. We found that limiting promoter search to such regions " "drastically reduces false positive predictions. Also, we have very strong " "thresholds for prediction of TATA-less promoters to minimize false positive " "predictions. </P>" " " "<P>\"Our promoter prediction software accurately predicts about 50% promoters " "accurately with a small average deviation from true start site. Such accuracy " "makes possible experimental work with found promoter candidates. </P>" " " "<P>\"For 20 experimentally verified promoters on Chromosome 22, TSSW predicted " "15, placed 12 of them within (-150,+150) region from true TSS and 6 (30% of " "all promoters) - within -8,+2 region from true TSS.\" </P>"); } void doCpgIsland(struct trackDb *tdb, char *item) /* Print info on CpG Island. */ { char *table = tdb->table; boolean isExt = hHasField(database, table, "obsExp"); cartWebStart(cart, database, "CpG Island Info"); printf("<H2>CpG Island Info</H2>\n"); if (cgiVarExists("o")) { struct cpgIsland *island; struct cpgIslandExt *islandExt = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); int rowOffset = hOffsetPastBin(database, seqName, table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (isExt) { islandExt = cpgIslandExtLoad(row+rowOffset); island = (struct cpgIsland *)islandExt; } else island = cpgIslandLoad(row+rowOffset); if (! startsWith("CpG: ", island->name)) printf("<B>Name:</B> %s<BR>\n", island->name); bedPrintPos((struct bed *)island, 3, tdb); printf("<B>Size:</B> %d<BR>\n", island->chromEnd - island->chromStart); printf("<B>CpG count:</B> %d<BR>\n", island->cpgNum); printf("<B>C count plus G count:</B> %d<BR>\n", island->gcNum); printf("<B>Percentage CpG:</B> %1.1f%%<BR>\n", island->perCpg); printf("<B>Percentage C or G:</B> %1.1f%%<BR>\n", island->perGc); if (islandExt != NULL) printf("<B>Ratio of observed to expected CpG:</B> %1.2f<BR>\n", islandExt->obsExp); printf("<BR>\n"); cpgIslandFree(&island); } hFreeConn(&conn); } else { puts("<P>Click directly on a CpG island for specific information on that island</P>"); } printTrackHtml(tdb); } void htcIlluminaProbesAlign(char *item) /* If the click came from "show alignment" on the Illumina */ /* probes details page, show the standard alignment page. */ { struct psl *psl; struct dnaSeq *seq; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); char query[256], **row; int start; char *pslTable = cgiUsualString("pslTable", "illuminaProbesAlign"); char *seqTable = cgiUsualString("seqTable", "illuminaProbesSeq"); char *probeName = item; char *probeString; int rowOffset = hOffsetPastBin(database, seqName, pslTable); char title[1024]; safef(title, sizeof title, "Sequence %s", probeName); htmlFramesetStart(title); start = cartInt(cart, "o"); /* get psl */ sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", pslTable, probeName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", probeName, start); psl = pslLoad(row+rowOffset); sqlFreeResult(&sr); sqlSafef(query, sizeof(query), "select seq from %s where id = '%s'", seqTable, probeName); probeString = sqlNeedQuickString(conn, query); seq = newDnaSeq(probeString, strlen(probeString), probeName); hFreeConn(&conn); showSomeAlignment(psl, seq, gftDna, 0, seq->size, probeName, 0, 0); pslFree(&psl); freeDnaSeq(&seq); freeMem(probeString); } void doIlluminaProbes(struct trackDb *tdb, char *item) /* The details page of the Illumina Probes track. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); char query[256]; int start = cartInt(cart, "o"); genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chromStart = '%d'", tdb->table, item, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct bed *bed = bedLoad12(row+rowOffset); printf("<B>Probe ID:</B> %s<BR>\n", bed->name); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, bed->chrom, bed->chromStart+1, bed->chromEnd); printf("%s:%d-%d</A><BR>\n", bed->chrom, bed->chromStart+1, bed->chromEnd); printf("<B>Alignment Score:</B> %d<BR>\n", bed->score); if ((bed->itemRgb == 1) || (bed->itemRgb == 2)) /* The "show alignment" link. */ { char other[256]; char *pslTable = trackDbRequiredSetting(tdb, "pslTable"); char *seqTable = trackDbRequiredSetting(tdb, "seqTable"); safef(other, sizeof(other), "%d&pslTable=%s&seqTable=%s", bed->chromStart, pslTable, seqTable); hgcAnchor("htcIlluminaProbesAlign", item, other); printf("View Alignment</A><BR>\n"); } bedFree(&bed); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doSwitchDbTss(struct trackDb *tdb, char *item) /* Print SwitchDB TSS details. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); char query[256]; genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", tdb->table, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct switchDbTss tss; switchDbTssStaticLoad(row+rowOffset, &tss); printPosOnChrom(tss.chrom, tss.chromStart, tss.chromEnd, tss.strand, FALSE, item); printf("<B>Gene Model:</B> %s<BR>\n", tss.gmName); printf("<B>Gene Model Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, tss.chrom, tss.gmChromStart+1, tss.gmChromEnd); printf("%s:%d-%d</A><BR>\n", tss.chrom, tss.gmChromStart+1, tss.gmChromEnd); printf("<B>TSS Confidence Score:</B> %.1f<BR>\n", tss.confScore); printf("<B>Pseudogene TSS: </B>%s<BR>\n", (tss.isPseudo == 1) ? "Yes" : "No"); } else { puts("<P>Click directly on a TSS for specific information on that TSS</P>"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void printLines(FILE *f, char *s, int lineSize) /* Print s, lineSize characters (or less) per line. */ { int len = strlen(s); int start; int oneSize; for (start = 0; start < len; start += lineSize) { oneSize = len - start; if (oneSize > lineSize) oneSize = lineSize; mustWrite(f, s+start, oneSize); fputc('\n', f); } if (start != len) fputc('\n', f); } void showProteinPrediction(char *pepName, char *table) /* Fetch and display protein prediction. */ { /* checks both gbSeq and table */ aaSeq *seq = hGenBankGetPep(database, pepName, table); if (seq == NULL) { warn("Predicted peptide %s is not avaliable", pepName); } else { printf("<PRE><TT>"); printf(">%s\n", pepName); printLines(stdout, seq->dna, 50); printf("</TT></PRE>"); dnaSeqFree(&seq); } } boolean isGenieGeneName(char *name) /* Return TRUE if name is in form to be a genie name. */ { char *s, *e; int prefixSize; e = strchr(name, '.'); if (e == NULL) return FALSE; prefixSize = e - name; if (prefixSize > 3 || prefixSize == 0) return FALSE; s = e+1; if (!startsWith("ctg", s)) return FALSE; e = strchr(name, '-'); if (e == NULL) return FALSE; return TRUE; } char *hugoToGenieName(char *hugoName, char *table) /* Covert from hugo to genie name. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; static char buf[256], *name; sqlSafef(query, sizeof query, "select transId from %s where name = '%s'", table, hugoName); name = sqlQuickQuery(conn, query, buf, sizeof(buf)); hFreeConn(&conn); if (name == NULL) errAbort("Database inconsistency: couldn't find gene name %s in knownInfo", hugoName); return name; } void displayProteinPrediction(char *pepName, char *pepSeq) /* display a protein prediction. */ { printf("<PRE><TT>"); printf(">%s length=%d\n", pepName,(int)strlen(pepSeq)); printLines(stdout, pepSeq, 50); printf("</TT></PRE>"); } void htcTranslatedProtein(char *pepName) /* Display translated protein. */ { char *table = cartString(cart, "o"); /* checks both gbSeq and table */ aaSeq *seq = hGenBankGetPep(database, pepName, table); cartHtmlStart("Protein Translation"); if (seq == NULL) { warn("Predicted peptide %s is not avaliable", pepName); } else { displayProteinPrediction(pepName, seq->dna); dnaSeqFree(&seq); } } static struct genePred *getGenePredForPositionSql(char *table, char *geneName) /* find the genePred for the current gene using an SQL table*/ { struct genePred *gpList = NULL; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct genePred *gp; int rowOffset = hOffsetPastBin(database, seqName, table); sqlSafef(query, sizeof(query), "select * from %s where name = \"%s\"", table, geneName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { gp = genePredLoad(row+rowOffset); slAddHead(&gpList, gp); } sqlFreeResult(&sr); hFreeConn(&conn); return gpList; } struct genePred *getGenePredForPositionBigGene(struct trackDb *tdb, char *geneName) /* Find the genePred to the current gene using a bigGenePred. */ { char *fileName = cloneString(trackDbSetting(tdb, "bigDataUrl")); struct bbiFile *bbi = bigBedFileOpen(fileName); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, winStart, winEnd, 0, lm); struct genePred *gpList = NULL; for (bb = bbList; bb != NULL; bb = bb->next) { struct genePred *gp = (struct genePred *)genePredFromBigGenePred(seqName, bb); if (sameString(gp->name, geneName)) slAddHead(&gpList, gp); } lmCleanup(&lm); return gpList; } static struct trackDb *getCustomTrackTdb(char *table) /* Find the trackDb structure for a custom track table. */ { struct customTrack *ctList = getCtList(); struct customTrack *ct = NULL; for (ct = ctList; ct != NULL; ct = ct->next) if (sameString(table, ct->tdb->track)) return ct->tdb; return NULL; } static struct genePred *getGenePredForPosition(char *table, char *geneName) /* Build a genePred list for the given table and gene name. */ { struct genePred *gpList = NULL; if (isCustomTrack(table)) { struct trackDb *tdb = getCustomTrackTdb(table); gpList = getGenePredForPositionBigGene(tdb, geneName); } else if (isHubTrack(table)) { struct trackDb *tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash); gpList = getGenePredForPositionBigGene(tdb, geneName); } else { struct trackDb *tdb = hashFindVal(trackHash, table); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl) gpList = getGenePredForPositionBigGene(tdb, geneName); else gpList = getGenePredForPositionSql(table, geneName); } return gpList; } void htcTranslatedPredMRna(char *geneName) /* Translate virtual mRNA defined by genePred to protein and display it. */ { char *table = cartString(cart, "table"); struct genePred *gp = NULL; char protName[256]; char *prot = NULL; cartHtmlStart("Protein Translation from Genome"); gp = getGenePredForPosition(table, geneName); if (gp == NULL) errAbort("%s not found in %s when translating to protein", geneName, table); else if (gp->cdsStart == gp->cdsEnd) errAbort("No CDS defined: no protein translation for %s", geneName); prot = getPredMRnaProtSeq(gp); safef(protName, sizeof(protName), "%s_prot", geneName); displayProteinPrediction(protName, prot); freez(&prot); genePredFree(&gp); } void htcTranslatedMRna(struct trackDb *tdb, char *acc) /* Translate mRNA to protein and display it. */ { struct sqlConnection *conn = hAllocConn(database); struct genbankCds cds = getCds(conn, acc); struct dnaSeq *mrna = hGenBankGetMrna(database, acc, NULL); if (mrna == NULL) errAbort("mRNA sequence %s not found", acc); if (cds.end > mrna->size) errAbort("CDS bounds exceed length of mRNA for %s", acc); int protBufSize = ((cds.end-cds.start)/3)+4; char *prot = needMem(protBufSize); mrna->dna[cds.end] = '\0'; dnaTranslateSome(mrna->dna+cds.start, prot, protBufSize); cartHtmlStart("Protein Translation of mRNA"); displayProteinPrediction(acc, prot); } void getCdsInMrna(struct genePred *gp, int *retCdsStart, int *retCdsEnd) /* Given a gene prediction, figure out the * CDS start and end in mRNA coordinates. */ { int missingStart = 0, missingEnd = 0; int exonStart, exonEnd, exonSize, exonIx; int totalSize = 0; for (exonIx = 0; exonIx < gp->exonCount; ++exonIx) { exonStart = gp->exonStarts[exonIx]; exonEnd = gp->exonEnds[exonIx]; exonSize = exonEnd - exonStart; totalSize += exonSize; missingStart += exonSize - positiveRangeIntersection(exonStart, exonEnd, gp->cdsStart, exonEnd); missingEnd += exonSize - positiveRangeIntersection(exonStart, exonEnd, exonStart, gp->cdsEnd); } *retCdsStart = missingStart; *retCdsEnd = totalSize - missingEnd; } int genePredCdnaSize(struct genePred *gp) /* Return total size of all exons. */ { int totalSize = 0; int exonIx; for (exonIx = 0; exonIx < gp->exonCount; ++exonIx) { totalSize += (gp->exonEnds[exonIx] - gp->exonStarts[exonIx]); } return totalSize; } struct dnaSeq *getCdnaSeq(struct genePred *gp) /* Load in cDNA sequence associated with gene prediction. */ { int txStart = gp->txStart; struct dnaSeq *genoSeq = hDnaFromSeq(database, gp->chrom, txStart, gp->txEnd, dnaLower); struct dnaSeq *cdnaSeq; int cdnaSize = genePredCdnaSize(gp); int cdnaOffset = 0, exonStart, exonSize, exonIx; AllocVar(cdnaSeq); cdnaSeq->dna = needMem(cdnaSize+1); cdnaSeq->size = cdnaSize; for (exonIx = 0; exonIx < gp->exonCount; ++exonIx) { exonStart = gp->exonStarts[exonIx]; exonSize = gp->exonEnds[exonIx] - exonStart; memcpy(cdnaSeq->dna + cdnaOffset, genoSeq->dna + (exonStart - txStart), exonSize); cdnaOffset += exonSize; } assert(cdnaOffset == cdnaSeq->size); freeDnaSeq(&genoSeq); return cdnaSeq; } struct dnaSeq *getCdsSeq(struct genePred *gp) /* Load in genomic CDS sequence associated with gene prediction. */ { struct dnaSeq *genoSeq = hDnaFromSeq(database, gp->chrom, gp->cdsStart, gp->cdsEnd, dnaLower); struct dnaSeq *cdsSeq; int cdsSize = genePredCodingBases(gp); int cdsOffset = 0, exonStart, exonEnd, exonSize, exonIx; AllocVar(cdsSeq); cdsSeq->dna = needMem(cdsSize+1); cdsSeq->size = cdsSize; for (exonIx = 0; exonIx < gp->exonCount; ++exonIx) { genePredCdsExon(gp, exonIx, &exonStart, &exonEnd); exonSize = (exonEnd - exonStart); if (exonSize > 0) { memcpy(cdsSeq->dna + cdsOffset, genoSeq->dna + (exonStart - gp->cdsStart), exonSize); cdsOffset += exonSize; } } assert(cdsOffset == cdsSeq->size); freeDnaSeq(&genoSeq); if (gp->strand[0] == '-') reverseComplement(cdsSeq->dna, cdsSeq->size); return cdsSeq; } char *getPredMRnaProtSeq(struct genePred *gp) /* Get the predicted mRNA from the genome and translate it to a * protein. free returned string. */ { struct dnaSeq *cdsDna = getCdsSeq(gp); int protBufSize = (cdsDna->size/3)+4; char *prot = needMem(protBufSize); int offset = 0; /* get frame offset, if available and needed */ if (gp->exonFrames != NULL) { if (gp->strand[0] == '+' && gp->cdsStartStat != cdsComplete) offset = (3 - gp->exonFrames[0]) % 3; else if (gp->strand[0] == '-' && gp->cdsEndStat != cdsComplete) offset = (3 - gp->exonFrames[gp->exonCount-1]) % 3; } /* NOTE: this fix will not handle the case in which frame is shifted * internally or at multiple exons, as when frame-shift gaps occur in * an alignment of an mRNA to the genome. Going to have to come back * and address that later... (acs) */ dnaTranslateSome(cdsDna->dna+offset, prot, protBufSize); dnaSeqFree(&cdsDna); return prot; } void ncbiRefSeqSequence(char *itemName) { char *table = cartString(cart, "o"); struct dnaSeq *rnaSeq = getBaseColorSequence(itemName, table ); cartHtmlStart("RefSeq mRNA Sequence"); printf("<PRE><TT>"); printf(">%s\n", itemName); faWriteNext(stdout, NULL, rnaSeq->dna, rnaSeq->size); printf("</TT></PRE>"); } void htcGeneMrna(char *geneName) /* Display cDNA predicted from genome */ { char *table = cartString(cart, "o"); cartHtmlStart("Predicted mRNA from Genome"); struct genePred *gp, *gpList = getGenePredForPosition(table, geneName), *next; int cdsStart, cdsEnd; struct dnaSeq *seq; for(gp = gpList; gp; gp = next) { next = gp->next; seq = getCdnaSeq(gp); getCdsInMrna(gp, &cdsStart, &cdsEnd); toUpperN(seq->dna + cdsStart, cdsEnd - cdsStart); if (gp->strand[0] == '-') { reverseComplement(seq->dna, seq->size); } printf("<PRE><TT>"); printf(">%s\n", geneName); faWriteNext(stdout, NULL, seq->dna, seq->size); printf("</TT></PRE>"); genePredFree(&gp); freeDnaSeq(&seq); } } void htcRefMrna(char *geneName) /* Display mRNA associated with a refSeq gene. */ { /* check both gbSeq and refMrna */ struct dnaSeq *seq = hGenBankGetMrna(database, geneName, "refMrna"); if (seq == NULL) errAbort("RefSeq mRNA sequence %s not found", geneName); cartHtmlStart("RefSeq mRNA"); printf("<PRE><TT>"); faWriteNext(stdout, seq->name, seq->dna, seq->size); printf("</TT></PRE>"); dnaSeqFree(&seq); } void cartContinueRadio(char *var, char *val, char *defaultVal) /* Put up radio button, checking it if it matches val */ { char *oldVal = cartUsualString(cart, var, defaultVal); cgiMakeRadioButton(var, val, sameString(oldVal, val)); } void htcGeneInGenome(char *geneName) /* Put up page that lets user display genomic sequence * associated with gene. */ { char *tbl = cgiString("o"); cartWebStart(cart, database, "Genomic Sequence Near Gene"); printf("<H2>Get Genomic Sequence Near Gene</H2>"); puts("<P>" "Note: if you would prefer to get DNA for more than one feature of " "this track at a time, try the "); printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(FALSE, tbl)); puts("Table Browser</A> using the output format sequence."); printf("<FORM ACTION=\"%s\">\n\n", hgcName()); cartSaveSession(cart); cgiMakeHiddenVar("g", "htcDnaNearGene"); cgiContinueHiddenVar("i"); printf("\n"); cgiContinueHiddenVar("db"); printf("\n"); cgiContinueHiddenVar("c"); printf("\n"); cgiContinueHiddenVar("l"); printf("\n"); cgiContinueHiddenVar("r"); printf("\n"); cgiContinueHiddenVar("o"); printf("\n"); if (isCustomTrack(tbl) || startsWith("hub_", tbl)) hgSeqOptions(cart, database, tbl); else { struct trackDb *tdb = hashFindVal(trackHash, tbl); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl) { // we asssume that this is a bigGenePred table if we got here with it hgSeqFeatureRegionOptions(cart, TRUE, TRUE); hgSeqDisplayOptions(cart, TRUE, TRUE, FALSE); } else hgSeqOptions(cart, database, tbl); } cgiMakeButton("submit", "submit"); printf("</FORM>"); } void htcGeneAlignment(char *geneName) /* Put up page that lets user display genomic sequence * associated with gene. */ { cartWebStart(cart, database, "Aligned Annotated Genomic Sequence "); printf("<H2>Align a gene prediction to another species or the same species and view codons and translated proteins.</H2>"); printf("<FORM ACTION=\"%s\">\n\n", hgcName()); cartSaveSession(cart); cgiMakeHiddenVar("g", "htcDnaNearGene"); cgiContinueHiddenVar("i"); printf("\n"); cgiContinueHiddenVar("db"); printf("\n"); cgiContinueHiddenVar("c"); printf("\n"); cgiContinueHiddenVar("l"); printf("\n"); cgiContinueHiddenVar("r"); printf("\n"); cgiContinueHiddenVar("o"); printf("\n"); hgSeqOptions(cart, database, cgiString("o")); cgiMakeButton("submit", "submit"); printf("</FORM>"); } void toUpperExons(int startOffset, struct dnaSeq *seq, struct genePred *gp) /* Upper case bits of DNA sequence that are exons according to gp. */ { int s, e, size; int exonIx; int seqStart = startOffset, seqEnd = startOffset + seq->size; if (seqStart < gp->txStart) seqStart = gp->txStart; if (seqEnd > gp->txEnd) seqEnd = gp->txEnd; for (exonIx = 0; exonIx < gp->exonCount; ++exonIx) { s = gp->exonStarts[exonIx]; e = gp->exonEnds[exonIx]; if (s < seqStart) s = seqStart; if (e > seqEnd) e = seqEnd; if ((size = e - s) > 0) { s -= startOffset; if (s < 0 || s + size > seq->size) errAbort("Out of range! %d-%d not in %d-%d", s, s+size, 0, size); toUpperN(seq->dna + s, size); } } } static struct bed *getBedsFromBigBedRange(struct trackDb *tdb, char *geneName) /* get a list of beds from a bigBed in the current range */ { struct bbiFile *bbi; char *fileName = cloneString(trackDbSetting(tdb, "bigDataUrl")); bbi = bigBedFileOpen(fileName); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, winStart, winEnd, 0, lm); struct bed *bedList = NULL; char *bedRow[32]; char startBuf[16], endBuf[16]; for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, seqName, startBuf, endBuf, bedRow, ArraySize(bedRow)); struct bed *bed = bedLoadN(bedRow, 12); if (sameString(bed->name, geneName)) slAddHead(&bedList, bed); } lmCleanup(&lm); return bedList; } static int getSeqForBigGene(struct trackDb *tdb, char *geneName) /* Output sequence for a gene in a bigGenePred file. */ { struct hTableInfo *hti; AllocVar(hti); hti->hasCDS = TRUE; hti->hasBlocks = TRUE; hti->rootName = tdb->table; struct bed *bedList = getBedsFromBigBedRange(tdb, geneName); int itemCount = hgSeqBed(database, hti, bedList); freez(&hti); bedFreeList(&bedList); return itemCount; } void htcDnaNearGene( char *geneName) /* Fetch DNA near a gene. */ { cartWebStart(cart, database, "%s", geneName); char *table = cartString(cart, "o"); int itemCount; char *quotedItem = makeQuotedString(geneName, '\''); puts("<PRE>"); struct trackDb *tdb = NULL; if (isHubTrack(table)) { tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash); itemCount = getSeqForBigGene(tdb, geneName); } else if (isCustomTrack(table)) { tdb = getCustomTrackTdb(table); itemCount = getSeqForBigGene(tdb, geneName); } else { tdb = hashFindVal(trackHash, table); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl) { itemCount = getSeqForBigGene(tdb, geneName); } else { char constraints[256]; safef(constraints, sizeof(constraints), "name = %s", quotedItem); itemCount = hgSeqItemsInRange(database, table, seqName, winStart, winEnd, constraints); } } if (itemCount == 0) printf("\n# No results returned from query.\n\n"); puts("</PRE>"); freeMem(quotedItem); } void htcTrackHtml(struct trackDb *tdb) /* Handle click to display track html */ { cartWebStart(cart, database, "%s", tdb->shortLabel); printTrackHtml(tdb); } void doViralProt(struct trackDb *tdb, char *geneName) /* Handle click on known viral protein track. */ { struct sqlConnection *conn = hAllocConn(database); int start = cartInt(cart, "o"); struct psl *pslList = NULL; cartWebStart(cart, database, "Viral Gene"); printf("<H2>Viral Gene %s</H2>\n", geneName); printCustomUrl(tdb, geneName, TRUE); pslList = getAlignments(conn, "chr1_viralProt", geneName); htmlHorizontalLine(); printf("<H3>Protein Alignments</H3>"); printAlignments(pslList, start, "htcProteinAli", "chr1_viralProt", geneName); printTrackHtml(tdb); } static boolean pslTrimListToTargetRange(struct psl *pslList, int winStart, int winEnd, int *retQRangeStart, int *retQRangeEnd) /* If the current window overlaps the target coords of any psl(s) in pslList, then return TRUE and * set *retQRange{Start,End} to span all query coord ranges corresponding to target coord ranges. * errAbort if qName is not consistent across all psls. * Otherwise return FALSE and set *retQRange{Start,End} to -1. */ { boolean foundOverlap = FALSE; char *qName = NULL; int qRangeStart = -1, qRangeEnd = -1; struct psl *psl; for (psl = pslList; psl != NULL; psl = psl->next) { if (qName == NULL) qName = psl->qName; else if (differentString(qName, psl->qName)) errAbort("pslTrimListToTargetRange: inconsistent qName: got both '%s' and '%s'", qName, psl->qName); if (psl->tStart >= winStart && psl->tEnd <= winEnd) { foundOverlap = TRUE; if (qRangeStart < 0 || psl->qStart < qRangeStart) qRangeStart = psl->qStart; if (qRangeEnd < 0 || psl->qEnd > qRangeEnd) qRangeEnd = psl->qEnd; } else { struct psl *partPsl = pslTrimToTargetRange(psl, winStart, winEnd); if (partPsl) { foundOverlap = TRUE; if (qRangeStart < 0 || partPsl->qStart < qRangeStart) qRangeStart = partPsl->qStart; if (qRangeEnd < 0 || partPsl->qEnd > qRangeEnd) qRangeEnd = partPsl->qEnd; } } } *retQRangeStart = qRangeStart; *retQRangeEnd = qRangeEnd; return foundOverlap; } void doPslAltSeq(struct trackDb *tdb, char *item) /* Details for alignments between chromosomes and alt haplogtype or fix patch sequences. */ { char *chrom = cartString(cart, "c"); int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); genericHeader(tdb, item); printCustomUrl(tdb, item, TRUE); puts("<P>"); struct psl *pslList = getAlignmentsTName(conn, tdb->table, item, chrom); if (pslList) { printf("<B>Alignment of %s to %s:</B><BR>\n", item, pslList->tName); printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); char *hgsid = cartSessionId(cart); if (hgIsOfficialChromName(database, item)) { int rangeStart = 0, rangeEnd = 0; if (pslTrimListToTargetRange(pslList, winStart, winEnd, &rangeStart, &rangeEnd)) { printf("<A HREF='hgTracks?hgsid=%s&position=%s:%d-%d'>" "View corresponding position range on %s</A><BR>\n", hgsid, item, rangeStart+1, rangeEnd, item); } } char *altFix = item; if (!endsWith(altFix, "alt") && !endsWith(altFix, "fix")) altFix = pslList->tName; if (hgIsOfficialChromName(database, altFix)) printf("<A HREF=\"hgTracks?hgsid=%s&virtModeType=singleAltHaplo&singleAltHaploId=%s\">" "Show %s placed on its chromosome</A><BR>\n", hgsid, altFix, altFix); puts("<P><B>Alignment stats:</B><BR>"); // Sometimes inversions cause alignments to be split up; just sum up all the stats. int totalBlocks = 0, totalSize = 0, totalMatch = 0, totalMismatch = 0, totalN = 0; int totalTIns = 0, totalQIns = 0; struct psl *psl; for (psl = pslList; psl != NULL; psl = psl->next) { totalBlocks += psl->blockCount; int i; for (i=0; i < psl->blockCount; i++) totalSize += psl->blockSizes[i]; totalMatch += (psl->match + psl->repMatch); totalMismatch += psl->misMatch; totalN += psl->nCount; totalTIns += psl->tBaseInsert; totalQIns += psl->qBaseInsert; } printf("%d block(s) covering %d bases<BR>\n" "%d matching bases (%.2f%%)<BR>\n" "%d mismatching bases (%.2f%%)<BR>\n" "%d N bases(%.2f%%)<BR>\n" "%d bases inserted in %s<BR>\n" "%d bases inserted in %s<BR>\n", totalBlocks, totalSize, totalMatch, 100.0 * (totalMatch / (double)totalSize), totalMismatch, 100.0 * (totalMismatch / (double)totalSize), totalN, 100.0 * (totalN / (double)totalSize), totalTIns, pslList->tName, totalQIns, item); } else warn("Unable to find alignment for '%s' in table %s", item, tdb->table); printTrackHtml(tdb); hFreeConn(&conn); } void doPslDetailed(struct trackDb *tdb, char *item) /* Fairly generic PSL handler -- print out some more details about the * alignment. */ { int start = cartInt(cart, "o"); int total = 0, i = 0; struct psl *pslList = NULL; struct sqlConnection *conn = hAllocConn(database); genericHeader(tdb, item); printCustomUrl(tdb, item, TRUE); puts("<P>"); puts("<B>Alignment Summary:</B><BR>\n"); pslList = getAlignments(conn, tdb->table, item); printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); puts("<P>"); total = 0; for (i=0; i < pslList -> blockCount; i++) { total += pslList->blockSizes[i]; } printf("%d block(s) covering %d bases<BR>\n" "%d matching bases<BR>\n" "%d mismatching bases<BR>\n" "%d N bases<BR>\n" "%d bases inserted in %s<BR>\n" "%d bases inserted in %s<BR>\n" "score: %d<BR>\n", pslList->blockCount, total, pslList->match + pslList->repMatch, pslList->misMatch, pslList->nCount, pslList->tBaseInsert, hOrganism(database), pslList->qBaseInsert, item, pslScore(pslList)); printTrackHtml(tdb); hFreeConn(&conn); } void printEnsemblCustomUrl(struct trackDb *tdb, char *itemName, boolean encode, char *archive) /* Print Ensembl Gene URL. */ { char *shortItemName; // char *genomeStr = ""; unused variable char *genomeStrEnsembl = ""; struct sqlConnection *conn = hAllocConn(database); char cond_str[256], cond_str2[256], cond_str3[256]; char *proteinID = NULL; char *ensPep; char *chp; char ensUrl[256]; char *ensemblIdUrl = trackDbSettingOrDefault(tdb, "ensemblIdUrl", "http://www.ensembl.org"); /* shortItemName is the name without the "." + version */ shortItemName = cloneString(itemName); /* ensembl gene names are different from their usual naming scheme on ce6/ce11*/ if (! (startsWith("ce6", database) || startsWith("ce11", database))) { chp = strstr(shortItemName, "."); if (chp != NULL) *chp = '\0'; } genomeStrEnsembl = ensOrgNameFromScientificName(scientificName); if (genomeStrEnsembl == NULL) { warn("Organism %s not found!", organism); fflush(stdout); return; } /* print URL that links to Ensembl transcript details */ if (sameString(ensemblIdUrl, "http://www.ensembl.org") && archive != NULL) safef(ensUrl, sizeof(ensUrl), "http://%s.archive.ensembl.org/%s", archive, genomeStrEnsembl); else { /* trackDb ensemblIdUrl might be more than just top level URL, * simply take it as given, e.g. criGriChoV1 */ if (countChars(ensemblIdUrl, '/') > 2) safef(ensUrl, sizeof(ensUrl), "%s", ensemblIdUrl); else safef(ensUrl, sizeof(ensUrl), "%s/%s", ensemblIdUrl, genomeStrEnsembl); } char query[512]; char *geneName = NULL; if (hTableExists(database, "ensemblToGeneName")) { sqlSafef(query, sizeof(query), "select value from ensemblToGeneName where name='%s'", itemName); geneName = sqlQuickString(conn, query); } char *ensemblSource = NULL; if (hTableExists(database, "ensemblSource")) { sqlSafef(query, sizeof(query), "select source from ensemblSource where name='%s'", itemName); ensemblSource = sqlQuickString(conn, query); } sqlSafefFrag(query, sizeof(query), "name = \"%s\"", itemName); struct genePred *gpList = genePredReaderLoadQuery(conn, "ensGene", query); if (gpList && gpList->name2) { printf("<B>Ensembl Gene Link: </B>"); if ((strlen(gpList->name2) < 1) || sameString(gpList->name2, "noXref")) printf("none<BR>\n"); else { printf("<A HREF=\"%s/geneview?gene=%s\" " "target=_blank>%s</A><BR>", ensUrl, gpList->name2, gpList->name2); if (! (ensemblSource && differentString("protein_coding",ensemblSource))) { printf("<B>Ensembl Gene Tree: </B>"); printf("<A HREF=\"%s/Gene/Compara_Tree?g=%s&t=%s\" " "target=_blank>%s</A><br>", ensUrl, gpList->name2, shortItemName, gpList->name2); } } } genePredFreeList(&gpList); printf("<B>Ensembl Transcript: </B>"); printf("<A HREF=\"%s/transview?transcript=%s\" " "target=_blank>", ensUrl, shortItemName); printf("%s</A><br>", itemName); if (hTableExists(database, "superfamily")) { sqlSafefFrag(cond_str, sizeof(cond_str), "transcript_name='%s'", shortItemName); /* This is necessary, Ensembl kept changing their gene_xref table definition and content.*/ proteinID = NULL; if (hTableExists(database, "ensemblXref3")) { /* use ensemblXref3 for Ensembl data release after ensembl34d */ sqlSafefFrag(cond_str3, sizeof(cond_str3), "transcript='%s'", shortItemName); ensPep = sqlGetField(database, "ensemblXref3", "protein", cond_str3); if (ensPep != NULL) proteinID = ensPep; } if (hTableExists(database, "ensTranscript") && (proteinID == NULL)) { proteinID = sqlGetField(database, "ensTranscript", "translation_name", cond_str); } else { if (hTableExists(database, "ensGeneXref")) { proteinID = sqlGetField(database, "ensGeneXref","translation_name", cond_str); } else if (hTableExists(database, "ensemblXref2")) { proteinID = sqlGetField(database, "ensemblXref2","translation_name", cond_str); } else { if (hTableExists(database, "ensemblXref")) { proteinID=sqlGetField(database, "ensemblXref","translation_name",cond_str); } } } if (proteinID != NULL) { printf("<B>Ensembl Protein: </B>"); printf("<A HREF=\"%s/protview?peptide=%s\" target=_blank>", ensUrl, proteinID); printf("%s</A><BR>\n", proteinID); } #ifdef NOT /* get genomeStr to be used in Superfamily URL */ if (sameWord(organism, "human")) { genomeStr = "hs"; } else { if (sameWord(organism, "mouse")) { genomeStr = "mm"; } else { if (sameWord(organism, "rat")) { genomeStr = "rn"; } else { if (sameWord(organism, "dog")) { genomeStr = "dg"; } else { warn("Organism %s not found!", organism); return; } } } } /* superfamily does not update with ensGene updates, stop printing an invalid URL */ sqlSafefFrag(cond_str, "name='%s'", shortItemName); char *ans = sqlGetField(conn, database, "superfamily", "name", cond_str); if (ans != NULL) { /* double check to make sure trackDb is also updated to be in sync with existence of supfamily table */ struct trackDb *tdbSf = hashFindVal(trackHash, "superfamily"); if (tdbSf != NULL) { char supfamURL[512]; printf("<B>Superfamily Link: </B>"); safef(supfamURL, sizeof(supfamURL), "<A HREF=\"%s%s;seqid=%s\" target=_blank>", tdbSf->url, genomeStr, proteinID); printf("%s%s</A><BR>\n", supfamURL, proteinID); } } #endif } if (hTableExists(database, "ensGtp") && (proteinID == NULL)) { /* shortItemName removes version number but sometimes the ensGtp */ /* table has a transcript with version number so exact match not used */ sqlSafefFrag(cond_str2, sizeof(cond_str2), "transcript like '%s%%'", shortItemName); proteinID=sqlGetField(database, "ensGtp","protein",cond_str2); if (proteinID != NULL) { printf("<B>Ensembl Protein: </B>"); printf("<A HREF=\"%s/protview?peptide=%s\" target=_blank>", ensUrl,proteinID); printf("%s</A><BR>\n", proteinID); } else { printf("<B>Ensembl Protein: </B>none (non-coding)<BR>\n"); } } if (geneName) { printf("<B>Gene Name: </B>%s<BR>\n", geneName); freeMem(geneName); } if (ensemblSource) { printf("<B>Ensembl Type: </B>%s<BR>\n", ensemblSource); freeMem(ensemblSource); } freeMem(shortItemName); } void printEnsemblOrVegaCustomUrl(struct trackDb *tdb, char *itemName, boolean encode, char *archive) /* Print Ensembl Gene URL. */ { boolean isEnsembl = FALSE; boolean isVega = FALSE; boolean hasEnsGtp = FALSE; boolean hasVegaGtp = FALSE; char *shortItemName; char *genomeStrEnsembl = ""; struct sqlConnection *conn = hAllocConn(database); char cond_str[256], cond_str2[256]; char *geneID = NULL; char *proteinID = NULL; char *chp; char dbUrl[256]; char geneType[256]; char gtpTable[256]; if (startsWith("ens", tdb->table)) { isEnsembl = TRUE; safef(geneType, sizeof(geneType), "Ensembl"); safef(gtpTable, sizeof(gtpTable), "ensGtp"); if (hTableExists(database, gtpTable)) hasEnsGtp = TRUE; } else if (startsWith("vega", tdb->table)) { isVega = TRUE; safef(geneType, sizeof(geneType), "Vega"); safef(gtpTable, sizeof(gtpTable), "vegaGtp"); if (hTableExists(database, gtpTable)) hasVegaGtp = TRUE; } /* shortItemName is the name without the "." + version */ shortItemName = cloneString(itemName); /* ensembl gene names are different from their usual naming scheme on ce6/ce11*/ if (! (startsWith("ce6", database) || startsWith("ce11", database)) ) { chp = strstr(shortItemName, "."); if (chp != NULL) *chp = '\0'; } genomeStrEnsembl = ensOrgNameFromScientificName(scientificName); if (genomeStrEnsembl == NULL) { warn("Organism %s not found!", organism); fflush(stdout); return; } /* print URL that links to Ensembl or Vega transcript details */ if (isEnsembl) { if (archive != NULL) safef(dbUrl, sizeof(dbUrl), "http://%s.archive.ensembl.org/%s", archive, genomeStrEnsembl); else safef(dbUrl, sizeof(dbUrl), "http://www.ensembl.org/%s", genomeStrEnsembl); } else if (isVega) safef(dbUrl, sizeof(dbUrl), "http://vega.sanger.ac.uk/%s", genomeStrEnsembl); boolean nonCoding = FALSE; char query[512]; sqlSafefFrag(query, sizeof(query), "name = \"%s\"", itemName); struct genePred *gpList = genePredReaderLoadQuery(conn, tdb->table, query); if (gpList && (gpList->cdsStart == gpList->cdsEnd)) nonCoding = TRUE; genePredFreeList(&gpList); /* get gene and protein IDs */ if ((isEnsembl && hasEnsGtp) || (isVega && hasVegaGtp)) { /* shortItemName removes version number but sometimes the ensGtp */ /* table has a transcript with version number so exact match not used */ sqlSafefFrag(cond_str, sizeof(cond_str), "transcript like '%s%%'", shortItemName); geneID=sqlGetField(database, gtpTable,"gene",cond_str); sqlSafefFrag(cond_str2, sizeof(cond_str2), "transcript like '%s%%'", shortItemName); proteinID=sqlGetField(database, gtpTable,"protein",cond_str2); } /* Print gene, transcript and protein links */ if (geneID != NULL) { printf("<B>%s Gene: </B>", geneType); printf("<A HREF=\"%s/geneview?gene=%s\" " "target=_blank>%s</A><BR>", dbUrl, geneID, geneID); } printf("<B>%s Transcript: </B>", geneType); printf("<A HREF=\"%s/transview?transcript=%s\" " "target=_blank>%s</A><BR>", dbUrl, shortItemName, itemName); if (proteinID != NULL) { printf("<B>%s Protein: </B>", geneType); if (nonCoding) printf("none (non-coding)<BR>\n"); else printf("<A HREF=\"%s/protview?peptide=%s\" " "target=_blank>%s</A><BR>", dbUrl, proteinID, proteinID); } freeMem(shortItemName); } void doEnsemblGene(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up Ensembl Gene track info or Ensembl NonCoding track info. */ { char *dupe, *type, *words[16]; int wordCount; int start = cartInt(cart, "o"); char condStr[256]; char headerTitle[512]; if (itemForUrl == NULL) itemForUrl = item; dupe = cloneString(tdb->type); struct trackVersion *trackVersion = getTrackVersion(database, tdb->track); if ((trackVersion != NULL) && !isEmpty(trackVersion->version)) safef(headerTitle, sizeof(headerTitle), "%s - Ensembl %s", item, trackVersion->version); else safef(headerTitle, sizeof(headerTitle), "%s", item); genericHeader(tdb, headerTitle); wordCount = chopLine(dupe, words); char *archive = trackDbSetting(tdb, "ensArchive"); if (archive == NULL) { if ((trackVersion != NULL) && !isEmpty(trackVersion->dateReference)) { if (differentWord("current", trackVersion->dateReference)) archive = cloneString(trackVersion->dateReference); } } printEnsemblCustomUrl(tdb, itemForUrl, item == itemForUrl, archive); sqlSafefFrag(condStr, sizeof condStr, "name='%s'", item); struct sqlConnection *conn = hAllocConn(database); /* if this is a non-coding gene track, then print the biotype and the external ID */ if (sameWord(tdb->table, "ensGeneNonCoding")) { char query[256]; struct sqlResult *sr = NULL; char **row; sqlSafef(query, sizeof(query), "select biotype, extGeneId from %s where %s", tdb->table, condStr); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Gene Type:</B> %s<BR>\n", row[0]); printf("<B>External Gene ID:</B> %s<BR>\n", row[1]); } sqlFreeResult(&sr); } else { /* print CCDS if this is not a non-coding gene */ printCcdsForSrcDb(conn, item); printf("<BR>\n"); } if (hTableExists(database, "ensInfo")) { struct sqlResult *sr; char query[256], **row; struct ensInfo *info = NULL; sqlSafef(query, sizeof(query), "select * from ensInfo where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { info = ensInfoLoad(row); /* no need to print otherId field, this is the same as name 2 in the ensGene table and it is printed by showGenePos() */ /* convert the status to lower case */ tolowers(info->status); printf("<B>Ensembl Gene Type:</B> %s %s<BR>\n", info->status, info->class); printf("<B>Ensembl Gene:</B> %s<BR>\n", info->geneId); printf("<B>Ensembl Gene Description:</B> %s<BR>\n", info->geneDesc); ensInfoFree(&info); } sqlFreeResult(&sr); } /* skip the rest if this gene is not in ensGene */ sqlSafefFrag(condStr, sizeof condStr, "name='%s'", item); if (sqlGetField(database, tdb->table, "name", condStr) != NULL) { if (wordCount > 0) { type = words[0]; if (sameString(type, "genePred")) { char *pepTable = NULL, *mrnaTable = NULL; if (wordCount > 1) pepTable = words[1]; if (wordCount > 2) mrnaTable = words[2]; genericGenePredClick(conn, tdb, item, start, pepTable, mrnaTable); } } } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void printSuperfamilyCustomUrl(struct trackDb *tdb, char *itemName, boolean encode) /* Print Superfamily URL. */ { char *url = tdb->url; if (url != NULL && url[0] != 0) { char supfamURL[1024]; char *genomeStr; struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; printf("The corresponding protein %s has the following Superfamily domain(s):", itemName); printf("<UL>\n"); sqlSafef(query, sizeof query, "select description from sfDescription where proteinID='%s';", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); while (row != NULL) { printf("<li>%s", row[0]); row = sqlNextRow(sr); } sqlFreeResult(&sr); hFreeConn(&conn); printf("</UL>"); if (sameWord(organism, "human")) { genomeStr = "hs"; } else { if (sameWord(organism, "mouse")) { genomeStr = "mm"; } else { if (sameWord(organism, "rat")) { genomeStr = "rn"; } else { warn("Organism %s not found!", organism); return; } } } printf("<B>Superfamily Link: </B>"); safef(supfamURL, sizeof supfamURL, "<A HREF=\"%s%s;seqid=%s\" target=_blank>", url, genomeStr, itemName); printf("%s%s</A><BR><BR>\n", supfamURL, itemName); } } void doSuperfamily(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up Superfamily track info. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *chrom, *chromStart, *chromEnd; char *transcript; if (itemForUrl == NULL) itemForUrl = item; genericHeader(tdb, item); printSuperfamilyCustomUrl(tdb, itemForUrl, item == itemForUrl); if (hTableExists(database, "ensGeneXref")) { sqlSafefFrag(query, sizeof query, "translation_name='%s'", item); transcript = sqlGetField(database, "ensGeneXref", "transcript_name", query); sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from superfamily where name='%s';", transcript); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { chrom = row[0]; chromStart = row[1]; chromEnd = row[2]; printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, TRUE, transcript); } sqlFreeResult(&sr); } if (hTableExists(database, "ensemblXref3")) { sqlSafefFrag(query, sizeof query, "protein='%s'", item); transcript = sqlGetField(database, "ensemblXref3", "transcript", query); sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from superfamily where name='%s';", transcript); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { chrom = row[0]; chromStart = row[1]; chromEnd = row[2]; printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, TRUE, transcript); } sqlFreeResult(&sr); } printTrackHtml(tdb); } void doOmimAv(struct trackDb *tdb, char *avName) /* Process click on an OMIM AV. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *chp; char *omimId, *avSubFdId; char *avDescStartPos, *avDescLen; char *omimTitle = cloneString(""); char *geneSymbol = NULL; int iAvDescStartPos = 0; int iAvDescLen = 0; struct lineFile *lf; char *line; int lineSize; cartWebStart(cart, database, "%s (%s)", tdb->longLabel, avName); sqlSafef(query, sizeof(query), "select * from omimAv where name = '%s'", avName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in omimAv table - database inconsistency.", avName); sqlFreeResult(&sr); omimId = strdup(avName); chp = strstr(omimId, "."); *chp = '\0'; chp++; avSubFdId = chp; sqlSafef(query, sizeof(query), "select title, geneSymbol from hgFixed.omimTitle where omimId = %s", omimId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { omimTitle = cloneString(row[0]); geneSymbol = cloneString(row[1]); } sqlFreeResult(&sr); printf("<H4>OMIM <A HREF=\""); printEntrezOMIMUrl(stdout, atoi(omimId)); printf("\" TARGET=_blank>%s</A>: %s; %s</H4>\n", omimId, omimTitle, geneSymbol); sqlSafef(query, sizeof(query), "select startPos, length from omimSubField where omimId='%s' and subFieldId='%s' and fieldType='AV'", omimId, avSubFdId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in omimSubField table - database inconsistency.", avName); else { avDescStartPos = cloneString(row[0]); avDescLen = cloneString(row[1]); iAvDescStartPos = atoi(avDescStartPos); iAvDescLen = atoi(avDescLen); } sqlFreeResult(&sr); lf = lineFileOpen("/gbdb/hg17/omim/omim.txt", TRUE); lineFileSeek(lf,(size_t)(iAvDescStartPos), 0); lineFileNext(lf, &line, &lineSize); printf("<h4>"); printf(".%s %s ", avSubFdId, line); lineFileNext(lf, &line, &lineSize); printf("[%s]\n", line); printf("</h4>"); while ((lf->lineStart + lf->bufOffsetInFile) < (iAvDescStartPos + iAvDescLen)) { lineFileNext(lf, &line, &lineSize); printf("%s\n", line); } htmlHorizontalLine(); printTrackHtml(tdb); hFreeConn(&conn); } void doRgdQtl(struct trackDb *tdb, char *item) /* Put up RGD QTL info. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *otherDb = trackDbSetting(tdb, "otherDb"); char *qtlOrg; if (sameString(tdb->table, "rgdQtl")) qtlOrg = organism; else if (isNotEmpty(otherDb)) qtlOrg = hOrganism(otherDb); else qtlOrg = ""; genericHeader(tdb, item); printf("<B>%s QTL %s: ", qtlOrg, item); sqlSafef(query, sizeof(query), "select description from %sLink where name='%s';", tdb->table, item); sr = sqlMustGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("%s", row[0]); sqlFreeResult(&sr); printf("</B><BR>\n"); if (isNotEmpty(tdb->url)) { boolean gotId = FALSE; sqlSafef(query, sizeof(query), "select id from %sLink where name='%s';", tdb->table, item); sr = sqlMustGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *qtlId = row[0]; printf(gotId ? ", \n\t" : "<B>RGD QTL Report:</B> "); printf("<B><A HREF=\"%s%s\" target=_blank>", tdb->url, qtlId); printf("RGD:%s</A></B>", qtlId); gotId = TRUE; } if (gotId) printf("\n<BR>\n"); sqlFreeResult(&sr); } int start=cartInt(cart, "o"), end=cartInt(cart, "t"); struct bed *selectedPos=NULL, *otherPosList=NULL, *bed=NULL; sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd from %s where name='%s' " "order by (chromEnd-chromStart);", tdb->table, item); sr = sqlMustGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoad3(row); if (selectedPos == NULL && sameString(bed->chrom, seqName) && bed->chromStart == start && bed->chromEnd == end) selectedPos = bed; else slAddHead(&otherPosList, bed); } sqlFreeResult(&sr); if (selectedPos) printPosOnChrom(seqName, start, end, NULL, FALSE, item); if (otherPosList) printf("<BR>%s QTL %s is also mapped to these locations " "(largest genomic size first):</BR>\n", qtlOrg, item); for (bed = otherPosList; bed != NULL; bed = bed->next) { printf("<HR>"); printPosOnChrom(bed->chrom, bed->chromStart, bed->chromEnd, NULL, FALSE, item); } hFreeConn(&conn); printTrackHtml(tdb); } void printGadDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of a GAD entry. */ { int refPrinted = 0; boolean showCompleteGadList; struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *chrom, *chromStart, *chromEnd; struct dyString *currentCgiUrl; char *diseaseClass; char *url = tdb->url; if (url != NULL && url[0] != 0) { showCompleteGadList = FALSE; if (cgiOptionalString("showAllRef") != NULL) { if (sameWord(cgiOptionalString("showAllRef"), "Y") || sameWord(cgiOptionalString("showAllRef"), "y") ) { showCompleteGadList = TRUE; } } currentCgiUrl = cgiUrlString(); printf("<H3>Gene %s: ", itemName); sqlSafef(query, sizeof(query), "select geneName from gadAll where geneSymbol='%s';", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL)printf("%s", row[0]); printf("</H3>"); sqlFreeResult(&sr); printf("<B>Genetic Association Database: "); printf("%s</B>\n", itemName); printf("<BR><B>CDC HuGE Published Literature: "); printf("<A HREF=\"https://phgkb.cdc.gov/PHGKB/searchSummary.action" "?Mysubmit=Search&firstQuery=%s&__checkbox_gwas=true\" target=_blank>", itemName); printf("%s</A></B>\n", itemName); sqlSafef(query, sizeof(query), "select distinct g.omimId, o.title from gadAll g, hgFixed.omimTitle o where g.geneSymbol='%s' and g.omimId <>'.' and g.omimId=o.omimId", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) printf("<BR><B>OMIM: </B>"); while (row != NULL) { printf("<A HREF=\"%s%s\" target=_blank>", "https://www.ncbi.nlm.nih.gov/omim/", row[0]); printf("%s</B></A> %s\n", row[0], row[1]); row = sqlNextRow(sr); } sqlFreeResult(&sr); /* List disease classes associated with the gene */ sqlSafef(query, sizeof(query), "select distinct diseaseClass from gadAll where geneSymbol='%s' and association = 'Y' order by diseaseClass", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { diseaseClass = row[0]; printf("<BR><B>Disease Class: </B>"); printf("%s", diseaseClass); row = sqlNextRow(sr); } while (row != NULL) { diseaseClass = row[0]; printf(", %s", diseaseClass); row = sqlNextRow(sr); } sqlFreeResult(&sr); /* List diseases associated with the gene */ sqlSafef(query, sizeof(query), "select distinct broadPhen from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<BR><B>Positive Disease Associations: </B>"); printf("%s\n", row[0]); row = sqlNextRow(sr); } while (row != NULL) { printf(", %s\n", row[0]); row = sqlNextRow(sr); } sqlFreeResult(&sr); refPrinted = 0; sqlSafef(query, sizeof(query), "select broadPhen,reference,title,journal, pubMed, conclusion from gadAll where geneSymbol='%s' and association = 'Y' and title != '' order by broadPhen", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) printf("<BR><BR><B>Related Studies: </B><OL>"); while (row != NULL) { printf("<LI><B>%s </B>", row[0]); printf("<br>%s, %s, %s.\n", row[1], row[2], row[3]); if (!sameWord(row[4], "")) { printf(" [PubMed "); printf("<A HREF=\""); printEntrezPubMedUidAbstractUrl(stdout, atoi(row[4])); printf("\" target=_blank>%s</B></A>]\n", row[4]); } printf("<br><i>%s</i>\n", row[5]); printf("</LI>\n"); refPrinted++; if ((!showCompleteGadList) && (refPrinted >= 5)) break; row = sqlNextRow(sr); } sqlFreeResult(&sr); printf("</OL>"); if ((!showCompleteGadList) && (row != NULL)) { printf("<B>   more ... </B>"); printf("<A HREF=\"%s?showAllRef=Y&%s\">click here to view the complete list</A> ", hgcName(), currentCgiUrl->string); } sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd from gad where name='%s';", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { chrom = row[0]; chromStart = row[1]; chromEnd = row[2]; printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } sqlFreeResult(&sr); hFreeConn(&conn); } } void doGad(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up GAD track info. */ { genericHeader(tdb, item); printGadDetails(tdb, item, FALSE); printTrackHtml(tdb); } void printCosmicDetails(struct trackDb *tdb, char *itemName) /* Print details of a COSMIC entry. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); char query[1024]; char query2[1024]; struct sqlResult *sr; struct sqlResult *sr2; char **row; char **row2; char *chp; char indent1[40] = {" "}; char indent2[40] = {""}; char *gene_name, *accession_number; // char $source, *cosmic_mutation_id; unused variable char *mut_description, *mut_syntax_cds, *mut_syntax_aa; char *chromosome, *grch37_start, *grch37_stop, *mut_nt; char *mut_aa, *tumour_site, *mutated_samples, *examined_samples, *mut_freq; char *url = tdb->url; char *chrom, *chromStart, *chromEnd; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); sqlSafef(query, sizeof(query), "select source,cosmic_mutation_id,gene_name,accession_number,mut_description,mut_syntax_cds,mut_syntax_aa," "chromosome,grch37_start,grch37_stop,mut_nt,mut_aa,tumour_site,mutated_samples,examined_samples,mut_freq" " from cosmicRaw where cosmic_mutation_id='%s'", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { int ii; boolean multipleTumorSites; char *indentString; ii=0; ii++; // source = row[ii];ii++; unused variable ii++; // cosmic_mutation_id = row[ii];ii++; unused variable gene_name = row[ii];ii++; accession_number = row[ii];ii++; mut_description = row[ii];ii++; mut_syntax_cds = row[ii];ii++; mut_syntax_aa = row[ii];ii++; chromosome = row[ii];ii++; grch37_start = row[ii];ii++; grch37_stop = row[ii];ii++; mut_nt = row[ii];ii++; mut_aa = row[ii];ii++; tumour_site = row[ii];ii++; mutated_samples = row[ii];ii++; examined_samples = row[ii];ii++; mut_freq = row[ii];ii++; // chromosome name adjustment if (sameString(chromosome, "23")) chromosome = "X"; if (sameString(chromosome, "24")) chromosome = "Y"; if (sameString(chromosome, "25")) chromosome = "M"; chp = strstr(itemName, "COSM")+strlen("COSM"); printf("<B>COSMIC ID:</B> <A HREF=\"%s%s\" TARGET=_BLANK>%s</A> (details at COSMIC site)", url, chp, chp); // Embed URL to COSMIC site per COSMICT request. // printf("<BR><B>Source:</B> "); // printf("<A HREF=\"http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/\" TARGET=_BLANK>%s</A>\n", source); printf("<BR><B>Gene Name:</B> %s\n", gene_name); printf("<BR><B>Accession Number:</B> %s\n", accession_number); printf("<BR><B>Genomic Position:</B> chr%s:%s-%s", chromosome, grch37_start, grch37_stop); printf("<BR><B>Mutation Description:</B> %s\n", mut_description); printf("<BR><B>Mutation Syntax CDS:</B> %s\n", mut_syntax_cds); printf("<BR><B>Mutation Syntax AA:</B> %s\n", mut_syntax_aa); printf("<BR><B>Mutation NT:</B> %s\n", mut_nt); printf("<BR><B>Mutation AA:</B> %s\n", mut_aa); sqlSafef(query2, sizeof(query2), "select count(tumour_site) from cosmicRaw where cosmic_mutation_id='%s'", itemName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if ((atoi(row2[0])) > 1) { multipleTumorSites = TRUE; indentString = indent1; } else { multipleTumorSites = FALSE; indentString = indent2; } sqlFreeResult(&sr2); sqlSafef(query2, sizeof(query2), "select tumour_site,mutated_samples,examined_samples,mut_freq " " from cosmicRaw where cosmic_mutation_id='%s' order by tumour_site", itemName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { int ii; ii=0; tumour_site = row2[ii];ii++; mutated_samples = row2[ii];ii++; examined_samples = row2[ii];ii++; mut_freq = row2[ii];ii++; if (multipleTumorSites) printf("<BR>"); printf("<BR><B>%sTumor Site:</B> %s\n", indentString, tumour_site); printf("<BR><B>%sMutated Samples:</B> %s\n", indentString, mutated_samples); printf("<BR><B>%sExamined Samples:</B> %s\n", indentString, examined_samples); printf("<BR><B>%sMutation Frequency:</B> %s\n", indentString, mut_freq); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); sqlSafef(query2, sizeof(query2), "select sum(mutated_samples) from cosmicRaw where cosmic_mutation_id='%s'", itemName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { printf("<BR><BR><B>Total Mutated Samples:</B> %s\n", row2[0]); //printf("<br>%s ", row2[0]); } sqlFreeResult(&sr2); sqlSafef(query2, sizeof(query2), "select sum(examined_samples) from cosmicRaw where cosmic_mutation_id='%s'", itemName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { printf("<BR><B>Total Examined Samples:</B> %s\n", row2[0]); } sqlFreeResult(&sr2); sqlSafef(query2, sizeof(query2), "select sum(mutated_samples)*100/sum(examined_samples) from cosmicRaw where cosmic_mutation_id='%s'", itemName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { char *chp; chp = strstr(row2[0], "."); if ((chp != NULL) && (strlen(chp) > 3)) { chp++; chp++; chp++; chp++; *chp = '\0'; } printf("<BR><B>Total Mutation Frequency:</B> %s%c\n", row2[0], '%'); //printf("<br>%s", row2[0]); } sqlFreeResult(&sr2); } sqlFreeResult(&sr); hFreeConn(&conn); printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } void doCosmic(struct trackDb *tdb, char *item) /* Put up COSMIC track info. */ { genericHeader(tdb, item); printCosmicDetails(tdb, item); printTrackHtml(tdb); } void printDecipherSnvsDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of a DECIPHER entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *strand={"+"}; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *chrom = cartString(cart, "c"); /* So far, we can just remove "chr" from UCSC chrom names to get DECIPHER names */ char *decipherChrom = chrom; if (startsWithNoCase("chr", decipherChrom)) decipherChrom += 3; printf("<H3>Patient %s </H3>", itemName); /* print phenotypes and other information, if available */ if (sqlFieldIndex(conn, "decipherSnvsRaw", "phenotypes") >= 0) { sqlSafef(query, sizeof(query), "select phenotypes, refAllele, altAllele, transcript, gene, genotype, " "inheritance, pathogenicity, contribution " "from decipherSnvsRaw where id = '%s' and chr = '%s' and start = %d and end = %d", itemName, decipherChrom, start+1, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if ((row != NULL) && strlen(row[0]) >= 1) { char *phenoString = replaceChars(row[0], "|", "</li>\n<li>"); printf("<b>Phenotypes:</b>\n<ul>\n" "<li>%s</li>\n" "</ul>\n", phenoString); // freeMem(phenoString); } if (row != NULL) { char *hgsidString = cartSidUrlString(cart); if (isNotEmpty(row[1])) { printf("<b>Ref Allele:</b> %s\n<br>\n", row[1]); } if (isNotEmpty(row[2])) { printf("<b>Alt Allele:</b> %s\n<br>\n", row[2]); } if (isNotEmpty(row[3])) { printf("<b>Transcript:</b> <a href='../cgi-bin/hgTracks?%s&position=%s'>%s</a>\n<br>\n", hgsidString, row[3], row[3]); } if (isNotEmpty(row[4])) { printf("<b>Gene:</b> <a href='../cgi-bin/hgTracks?%s&position=%s'>%s</a>\n<br>\n", hgsidString, row[4], row[4]); } if (isNotEmpty(row[5])) { printf("<b>Genotype:</b> %s\n<br>\n", row[5]); } if (isNotEmpty(row[6])) { printf("<b>Inheritance:</b> %s\n<br>\n", row[6]); } if (isNotEmpty(row[7])) { printf("<b>Pathogenicity:</b> %s\n<br>\n", row[7]); } if (isNotEmpty(row[8])) { printf("<b>Contribution:</b> %s\n<br>\n", row[8]); } } sqlFreeResult(&sr); } else { sqlSafef(query, sizeof(query), "select distinct phenotype from decipherSnvsRaw where id ='%s' order by phenotype", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if ((row != NULL) && strlen(row[0]) >= 1) { printf("<B>Phenotype: </B><UL>"); while (row != NULL) { printf("<LI>"); printf("%s\n", row[0]); row = sqlNextRow(sr); } printf("</UL>"); } sqlFreeResult(&sr); } /* link to Ensembl DECIPHER Patient View page */ printf("<B>Patient View: </B>\n"); printf("More details on patient %s at ", itemName); printf("<A HREF=\"%s%s\" target=_blank>", "https://decipher.sanger.ac.uk/patient/", itemName); printf("DECIPHER</A>.<BR><BR>"); /* print position info */ printPosOnChrom(chrom, start, end, strand, TRUE, itemName); hFreeConn(&conn); } void doDecipherSnvs(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up DECIPHER track info. */ { genericHeader(tdb, item); printDecipherSnvsDetails(tdb, item, FALSE); printTrackHtml(tdb); } void printDecipherCnvsDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of a DECIPHER entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; struct sqlConnection *conn2 = hAllocConn(database); char query2[256]; struct sqlResult *sr2; char **row2; char *strand={"+"}; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *chrom = cartString(cart, "c"); /* So far, we can just remove "chr" from UCSC chrom names to get DECIPHER names */ char *decipherChrom = chrom; if (startsWithNoCase("chr", decipherChrom)) decipherChrom += 3; printf("<H3>Patient %s </H3>", itemName); /* print phenotypes and other information, if available */ if (sqlFieldIndex(conn, "decipherRaw", "phenotypes") >= 0) { sqlSafef(query, sizeof(query), "select phenotypes, mean_ratio, inheritance, pathogenicity, contribution " "from decipherRaw where id = '%s' and chr = '%s' and start = %d and end = %d", itemName, decipherChrom, start+1, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if ((row != NULL) && strlen(row[0]) >= 1) { char *phenoString = replaceChars(row[0], "|", "</li>\n<li>"); printf("<b>Phenotypes:</b>\n<ul>\n" "<li>%s</li>\n" "</ul>\n", phenoString); // freeMem(phenoString); } if (row != NULL) { if (isNotEmpty(row[1])) { printf("<b>Mean Ratio:</b> %s\n<br>\n", row[1]); } if (isNotEmpty(row[2])) { printf("<b>Inheritance:</b> %s\n<br>\n", row[2]); } if (isNotEmpty(row[3])) { printf("<b>Pathogenicity:</b> %s\n<br>\n", row[3]); } if (isNotEmpty(row[4])) { printf("<b>Contribution:</b> %s\n<br>\n", row[4]); } } sqlFreeResult(&sr); } else { sqlSafef(query, sizeof(query), "select distinct phenotype from decipherRaw where id ='%s' order by phenotype", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if ((row != NULL) && strlen(row[0]) >= 1) { printf("<B>Phenotype: </B><UL>"); while (row != NULL) { printf("<LI>"); printf("%s\n", row[0]); row = sqlNextRow(sr); } printf("</UL>"); } sqlFreeResult(&sr); } /* link to Ensembl DECIPHER Patient View page */ printf("<B>Patient View: </B>\n"); printf("More details on patient %s at ", itemName); printf("<A HREF=\"%s%s\" target=_blank>", "https://decipher.sanger.ac.uk/patient/", itemName); printf("DECIPHER</A>.<BR><BR>"); /* print position info */ printPosOnChrom(chrom, start, end, strand, TRUE, itemName); /* print UCSC Genes in the reported region */ sqlSafef(query, sizeof(query), "select distinct t.name " // mysql 5.7: SELECT list w/DISTINCT must include all fields in ORDER BY list (#18626) ", geneSymbol " "from knownCanonToDecipher t, kgXref x where value ='%s' and x.kgId=t.name order by geneSymbol", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<BR><B>UCSC Canonical Gene(s) in this genomic region: </B><UL>"); while (row != NULL) { sqlSafef(query2, sizeof(query2), "select geneSymbol, kgId, description from kgXref where kgId ='%s'", row[0]); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { printf("<LI>"); printf("<A HREF=\"%s%s\" target=_blank>","./hgGene\?hgg_chrom=none&hgg_gene=", row2[1]); printf("%s (%s)</A> ", row2[0], row2[1]); printf(" %s", row2[2]); } sqlFreeResult(&sr2); row = sqlNextRow(sr); } sqlFreeResult(&sr); printf("</UL>"); } hFreeConn(&conn); hFreeConn(&conn2); } void doDecipherCnvs(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up DECIPHER track info. */ { genericHeader(tdb, item); printDecipherCnvsDetails(tdb, item, FALSE); printTrackHtml(tdb); } char *gbCdnaGetDescription(struct sqlConnection *conn, char *acc) /* return mrna description, or NULL if not available. freeMem result */ { char query[1024]; if (!sqlTableExists(conn, gbCdnaInfoTable)) return NULL; sqlSafef(query, sizeof(query), "select d.name from %s g,%s d where (acc = '%s') and (g.description = d.id)", gbCdnaInfoTable, descriptionTable, acc); char *desc = sqlQuickString(conn, query); if ((desc == NULL) || sameString(desc, "n/a") || (strlen(desc) == 0)) freez(&desc); return desc; } void printOmimGeneDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an OMIM Gene entry. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *kgId= NULL; char *title1 = NULL; char *geneSymbols = NULL; char *chrom, *chromStart, *chromEnd; char *kgDescription = NULL; char *refSeq; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); if (url != NULL && url[0] != 0) { /* check if the entry is in morbidmap, if so remember the assoicated gene symbols */ sqlSafef(query, sizeof(query), "select geneSymbols from omimMorbidMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { geneSymbols = cloneString(row[0]); } sqlFreeResult(&sr); /* get corresponding KG ID */ sqlSafef(query, sizeof(query), "select k.transcript from knownCanonical k where k.chrom='%s' and k.chromStart=%s and k.chromEnd=%s", chrom, chromStart, chromEnd); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { kgId = cloneString(row[0]); } sqlFreeResult(&sr); /* use geneSymbols from omimMorbidMap if available */ if (geneSymbols!= NULL) { printf("<B>OMIM gene or syndrome:</B> %s", geneSymbols); printf("<BR>\n"); /* display disorder for genes in morbidmap */ sqlSafef(query, sizeof(query), "select description from omimMorbidMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("<B>Disorder:</B> %s", row[0]); printf("<BR>\n"); } sqlFreeResult(&sr); } else { /* display gene symbol(s) from omimGeneMap2 */ sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<B>OMIM Gene Symbol:</B> %s", row[0]); printf("<BR>\n"); sqlFreeResult(&sr); } else { /* get gene symbol from kgXref if the entry is not in morbidmap and omim genemap */ sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<B>UCSC Gene Symbol:</B> %s", row[0]); printf("<BR>\n"); } sqlFreeResult(&sr); } } printf("<B>OMIM Database "); printf("<A HREF=\"%s%s\" target=_blank>", url, itemName); printf("%s</A></B>", itemName); sqlSafef(query, sizeof(query), "select geneName from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { title1 = cloneString(row[0]); printf(": %s", title1); } } sqlFreeResult(&sr); printf("<BR>\n"); if (kgId != NULL) { printf("<B>UCSC Canonical Gene "); printf("<A HREF=\"%s%s&hgg_chrom=none\" target=_blank>", "../cgi-bin/hgGene?hgg_gene=", kgId); printf("%s</A></B>: ", kgId); sqlSafef(query, sizeof(query), "select refseq from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { refSeq = strdup(row[0]); kgDescription = gbCdnaGetDescription(conn2, refSeq); } sqlFreeResult(&sr); hFreeConn(&conn2); if (kgDescription == NULL) { sqlSafef(query, sizeof(query), "select description from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("%s", row[0]); } sqlFreeResult(&sr); } else { printf("%s", kgDescription); } printf("<BR>\n"); sqlSafef(query, sizeof(query), "select i.transcript from knownIsoforms i, knownCanonical c where c.transcript='%s' and i.clusterId=c.clusterId and i.transcript <>'%s'", kgId, kgId); sr = sqlMustGetResult(conn, query); if (sr != NULL) { int printedCnt; printedCnt = 0; while ((row = sqlNextRow(sr)) != NULL) { if (printedCnt < 1) printf("<B>Other UCSC Gene(s) in the same cluster: </B>"); else printf(", "); printf("<A HREF=\"%s%s&hgg_chrom=none\" target=_blank>", "../cgi-bin/hgGene?hgg_gene=", row[0]); printf("%s</A></B>", row[0]); printedCnt++; } if (printedCnt >= 1) printf("<BR>\n"); } sqlFreeResult(&sr); } } printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } #include "omim.h" static void showOmimDisorderTable(struct sqlConnection *conn, char *url, char *itemName) { /* display disorder(s) as a table, in the same format as on the OMIM webpages, * e.g. see the "Gene-Phenotype-Relationships" table at https://www.omim.org/entry/601542 */ struct sqlResult *sr; char query[256]; char **row; // be tolerant of old table schema if (sqlColumnExists(conn, "omimPhenotype", "inhMode")) sqlSafef(query, sizeof(query), "select description, %s, phenotypeId, inhMode from omimPhenotype where omimId=%s order by description", omimPhenotypeClassColName, itemName); else // E.g. on a mirror that has not updated their OMIM tables yet sqlSafef(query, sizeof(query), "select description, %s, phenotypeId, 'data-missing' from omimPhenotype where omimId=%s order by description", omimPhenotypeClassColName, itemName); sr = sqlMustGetResult(conn, query); char *phenotypeClass, *phenotypeId, *disorder, *inhMode; printf("<table class='omimTbl'>\n"); printf("<thead>\n"); printf("<th>Phenotype</th>\n"); printf("<th style='width:100px'>Phenotype MIM Number</th>\n"); printf("<th>Inheritance</th>\n"); printf("<th>Phenotype Key</th>\n"); printf("</thead>\n"); printf("<tbody>\n"); while ((row = sqlNextRow(sr)) != NULL) { disorder = row[0]; phenotypeClass = row[1]; phenotypeId = row[2]; inhMode = row[3]; puts("<tr>\n"); puts("<td>"); if (disorder) puts(disorder); puts("</td>\n"); puts("<td>"); if (phenotypeId && (!sameWord(phenotypeId, "-1"))) printf("<a HREF=\"%s%s\" target=_blank>%s</a>", url, phenotypeId, phenotypeId); puts("</td>\n"); puts("<td>"); if (inhMode) puts(inhMode); puts("</td>"); puts("<td>"); if (phenotypeClass && !sameWord(phenotypeClass, "-1")) { puts(phenotypeClass); if (isdigit(phenotypeClass[0])) { int phenoClass = atoi(phenotypeClass); char* descs[] = { "disease was positioned by mapping of the wild-type gene", "disorder itself was mapped", "molecular basis of the disease is known", "disorder is a chromosome deletion of duplication syndrome" }; if (phenoClass>=1 && phenoClass<=4) { puts(" - "); puts(descs[phenoClass-1]); } else // just in case that they ever add another class in the future puts(phenotypeClass); } } puts("</td>"); puts("</tr>"); } sqlFreeResult(&sr); printf("<tbody>\n"); printf("</table>\n"); } void printOmimGene2Details(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an omimGene2 entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; -char *title1 = NULL; -char *geneSymbol = NULL; char *chrom, *chromStart, *chromEnd; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); printf("<div id='omimText'>"); if (url != NULL && url[0] != 0) { printf("<B>MIM gene number: "); printf("<A HREF=\"%s%s\" target=_blank>", url, itemName); - printf("%s</A></B>", itemName); - sqlSafef(query, sizeof(query), - "select geneName from omimGeneMap2 where omimId=%s;", itemName); - sr = sqlMustGetResult(conn, query); - row = sqlNextRow(sr); - if (row != NULL) - { - if (row[0] != NULL) - { - title1 = cloneString(row[0]); - printf(" %s", title1); - } - } - else - { - printf("<BR>"); - } - sqlFreeResult(&sr); + printf("%s</A></B><BR>", itemName); // disable NCBI link until they work it out with OMIM /* printf("<BR>\n"); printf("<B>OMIM page at NCBI: "); printf("<A HREF=\"%s%s\" target=_blank>", ncbiOmimUrl, itemName); printf("%s</A></B>", itemName); */ - // can use NOSQLINJ since itemName has already been checked to be a number struct dyString *symQuery = newDyString(1024); sqlDyStringPrintf(symQuery, "SELECT approvedSymbol from omimGeneMap2 where omimId=%s", itemName); char *approvSym = sqlQuickString(conn, symQuery->string); if (approvSym) { - printf("<BR><B>HGNC-approved symbol:</B> %s<BR>", approvSym); - freez(&approvSym); + printf("<B>HGNC-approved symbol:</B> %s", approvSym); } + + sqlSafef(query, sizeof(query), + "select geneName from omimGeneMap2 where omimId=%s;", itemName); + char *longName = sqlQuickString(conn, query); + if (longName) { + printf(" — %s", longName); + freez(&longName); + } + puts("<BR>"); + printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 where omimId=%s;", itemName); - sr = sqlMustGetResult(conn, query); - row = sqlNextRow(sr); - if (row != NULL) - { - geneSymbol = cloneString(row[0]); - } - sqlFreeResult(&sr); + char *altSyms = sqlQuickString(conn, query); - if (geneSymbol!= NULL) + if (altSyms) + { + if (approvSym) { - printf("<BR><B>Alternative symbols:</B> %s", geneSymbol); + char symRe[255]; + safef(symRe, sizeof(symRe), "^%s, ", approvSym); + altSyms = replaceRegEx(altSyms, "", symRe, 0); + } + printf("<B>Alternative symbols:</B> %s", altSyms); printf("<BR>\n"); + freez(&altSyms); } + if (approvSym) + freez(&approvSym); // show RefSeq Gene link(s) sqlSafef(query, sizeof(query), "select distinct locusLinkId from %s l, omim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s", refLinkTable, itemName, chrom, chromStart, chromEnd); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { char *geneId; geneId = strdup(row[0]); sqlFreeResult(&sr); sqlSafef(query, sizeof(query), "select distinct l.mrnaAcc from %s l where locusLinkId = '%s' order by mrnaAcc asc", refLinkTable, geneId); sr = sqlMustGetResult(conn, query); if (sr != NULL) { int printedCnt; printedCnt = 0; while ((row = sqlNextRow(sr)) != NULL) { if (printedCnt < 1) printf("<B>RefSeq Gene(s): </B>"); else printf(", "); printf("<A HREF=\"%s%s&o=%s&t=%s\">", "../cgi-bin/hgc?g=refGene&i=", row[0], chromStart, chromEnd); printf("%s</A></B>", row[0]); printedCnt++; } if (printedCnt >= 1) printf("<BR>\n"); } sqlFreeResult(&sr); } // show Related UCSC Gene links sqlSafef(query, sizeof(query), "select distinct kgId from kgXref x, %s l, omim2gene g where x.refseq = mrnaAcc and l.omimId=%s and g.omimId=l.omimId and g.entryType='gene'", refLinkTable, itemName); sr = sqlMustGetResult(conn, query); if (sr != NULL) { int printedCnt; printedCnt = 0; while ((row = sqlNextRow(sr)) != NULL) { if (printedCnt < 1) printf("<B>Related Transcripts: </B>"); else printf(", "); printf("<A HREF=\"%s%s&hgg_chrom=none\">", "../cgi-bin/hgGene?hgg_gene=", row[0]); printf("%s</A></B>", row[0]); printedCnt++; } if (printedCnt >= 1) printf("<BR>\n"); } sqlFreeResult(&sr); // show GeneReviews link(s) if (sqlTableExists(conn, "geneReviewsDetail")) { sqlSafef(query, sizeof(query), "select distinct r.name2 from %s l, omim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s", refLinkTable, itemName, chrom, chromStart, chromEnd); sr = sqlMustGetResult(conn, query); if (sr != NULL) { while ((row = sqlNextRow(sr)) != NULL) { prGRShortRefGene(row[0]); } } sqlFreeResult(&sr); } showOmimDisorderTable(conn, url, itemName); } printf("</div>"); // #omimText } void printOmimLocationDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an OMIM Class 3 Gene entry. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *kgId= NULL; char *title1 = NULL; char *geneSymbol = NULL; char *chrom, *chromStart, *chromEnd; char *kgDescription = NULL; char *refSeq; char *omimId; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); omimId = itemName; if (url != NULL && url[0] != 0) { printf("<B>OMIM: "); printf("<A HREF=\"%s%s\" target=_blank>", url, itemName); printf("%s</A></B>", itemName); sqlSafef(query, sizeof(query), "select geneName from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { title1 = cloneString(row[0]); printf(": %s", title1); } } sqlFreeResult(&sr); printf("<BR>"); // disable NCBI link until they work it out with OMIM /* printf("<B>OMIM page at NCBI: "); printf("<A HREF=\"%s%s\" target=_blank>", ncbiOmimUrl, itemName); printf("%s</A></B><BR>", itemName); */ printf("<B>Location: </B>"); sqlSafef(query, sizeof(query), "select location from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { char *locStr; locStr= cloneString(row[0]); printf("%s\n", locStr); } } sqlFreeResult(&sr); printf("<BR>\n"); sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { geneSymbol = cloneString(row[0]); } sqlFreeResult(&sr); sqlSafef(query, sizeof(query),"select omimId from omimPhenotype where omimId=%s\n", omimId); if (sqlQuickNum(conn, query) > 0) { char *phenotypeClass, *phenotypeId, *disorder; printf("<B>Gene symbol(s):</B> %s", geneSymbol); printf("<BR>\n"); /* display disorder for genes in morbidmap */ sqlSafef(query, sizeof(query), "select description, %s, phenotypeId from omimPhenotype where omimId=%s order by description", omimPhenotypeClassColName, itemName); sr = sqlMustGetResult(conn, query); printf("<B>Disorder(s):</B><UL>\n"); while ((row = sqlNextRow(sr)) != NULL) { disorder = row[0]; phenotypeClass = row[1]; phenotypeId = row[2]; printf("<LI>%s", disorder); if (phenotypeId != NULL) { if (!sameWord(phenotypeId, "-1")) { printf(" (phenotype <A HREF=\"%s%s\" target=_blank>", url, phenotypeId); printf("%s</A></B>)", phenotypeId); } if (!sameWord(phenotypeClass, "-1")) { printf(" (%s)", phenotypeClass); } } printf("<BR>\n"); } printf("</UL>\n"); sqlFreeResult(&sr); } else { /* display gene symbol(s) from omimGenemap */ sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<B>OMIM Gene Symbol:</B> %s", row[0]); printf("<BR>\n"); sqlFreeResult(&sr); } else { /* get gene symbol from kgXref if the entry is not in morbidmap and omim genemap */ sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<B>UCSC Gene Symbol:</B> %s", row[0]); printf("<BR>\n"); } sqlFreeResult(&sr); } } if (kgId != NULL) { printf("<B>UCSC Canonical Gene "); printf("<A HREF=\"%s%s&hgg_chrom=none\" target=_blank>", "../cgi-bin/hgGene?hgg_gene=", kgId); printf("%s</A></B>: ", kgId); sqlSafef(query, sizeof(query), "select refseq from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { refSeq = strdup(row[0]); kgDescription = gbCdnaGetDescription(conn2, refSeq); } sqlFreeResult(&sr); hFreeConn(&conn2); if (kgDescription == NULL) { sqlSafef(query, sizeof(query), "select description from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("%s", row[0]); } sqlFreeResult(&sr); } else { printf("%s", kgDescription); } printf("<BR>\n"); sqlSafef(query, sizeof(query), "select i.transcript from knownIsoforms i, knownCanonical c where c.transcript='%s' and i.clusterId=c.clusterId and i.transcript <>'%s'", kgId, kgId); sr = sqlMustGetResult(conn, query); if (sr != NULL) { int printedCnt; printedCnt = 0; while ((row = sqlNextRow(sr)) != NULL) { if (printedCnt < 1) printf("<B>Other UCSC Gene(s) in the same cluster: </B>"); else printf(", "); printf("<A HREF=\"%s%s&hgg_chrom=none\" target=_blank>", "../cgi-bin/hgGene?hgg_gene=", row[0]); printf("%s</A></B>", row[0]); printedCnt++; } if (printedCnt >= 1) printf("<BR>\n"); } sqlFreeResult(&sr); } } printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } void doOmimLocation(struct trackDb *tdb, char *item) /* Put up OmimGene track info. */ { genericHeader(tdb, item); printOmimLocationDetails(tdb, item, FALSE); printTrackHtml(tdb); } void printOmimAvSnpDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an OMIM AvSnp entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *title1 = NULL; char *chrom, *chromStart, *chromEnd; char *avId; char *dbSnpId; char *chp; char avString[255]; char *avDesc = NULL; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); avId = strdup(itemName); chp = strstr(avId, "-"); if (chp != NULL) *chp = '\0'; safef(avString, sizeof(avString), "%s", itemName); chp = strstr(itemName, "."); *chp = '\0'; chp = avString; chp = strstr(avString, "."); *chp = '#'; if (url != NULL && url[0] != 0) { sqlSafef(query, sizeof(query), "select m.geneName, format(seqNo/10000,4), v.description" " from omimGeneMap2 m, omimAv v" " where m.omimId=%s and m.omimId=v.omimId and v.avId='%s';", itemName, avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { title1 = cloneString(row[0]); } avDesc = cloneString(row[2]); } sqlFreeResult(&sr); printf("<B>OMIM Allelic Variant: "); printf("<A HREF=\"%s%s\" target=_blank>", url, avString); printf("%s</A></B>", avId); printf(" %s", avDesc); printf("<BR><B>OMIM: "); printf("<A HREF=\"%s%s\" target=_blank>", url, itemName); printf("%s</A></B>", itemName); if (title1 != NULL) printf(": %s", title1); // disable NCBI link until they work it out with OMIM /* printf("<BR>\n"); printf("<B>OMIM page at NCBI: "); printf("<A HREF=\"%s%s\" target=_blank>", ncbiOmimUrl, itemName); printf("%s</A></B><BR>", itemName); */ sqlSafef(query, sizeof(query), "select repl2 from omimAv where avId=%s;", avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) printf("<BR><B>Amino Acid Replacement:</B> %s\n", row[0]); } sqlFreeResult(&sr); printf("<BR>\n"); sqlSafef(query, sizeof(query), "select dbSnpId from omimAv where avId='%s'", avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); dbSnpId = cloneString("-"); if (row != NULL) dbSnpId = cloneString(row[0]); sqlFreeResult(&sr); if (!sameWord(dbSnpId, "-")) { struct slName *snpIdList, *thisSnpId; printf("<b>dbSNP/ClinVar:</b> \n"); /* for each variant, print name and build a link for it if possible */ snpIdList = slNameListFromComma(dbSnpId); while ((thisSnpId = slPopHead(&snpIdList)) != NULL) { if (strncmp(thisSnpId->name, "rs", 2) == 0) /* dbSnp ID */ printDbSnpRsUrl (thisSnpId->name, "%s", thisSnpId->name); else if (strncmp(thisSnpId->name, "SCV", 3) == 0) /* ClinVar ID */ { char clinVarUrl[2048]; safef (clinVarUrl, sizeof(clinVarUrl), clinVarFormat, thisSnpId->name); printf ("<a href=\"%s\" target=\"_blank\">%s</a>", clinVarUrl, thisSnpId->name); } else printf ("%s", thisSnpId->name); slNameFree(&thisSnpId); if (snpIdList != NULL) printf (","); } printf("<br>\n"); } } printf("<hr>\n"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } void doOmimAvSnp(struct trackDb *tdb, char *item) /* Put up OmimGene track info. */ { genericHeader(tdb, item); printOmimAvSnpDetails(tdb, item, FALSE); printTrackHtml(tdb); } void doOmimGene2(struct trackDb *tdb, char *item) /* Put up OmimGene track info. */ { cartWebStart(cart, database, "OMIM genes - %s", item); printOmimGene2Details(tdb, item, FALSE); printTrackHtml(tdb); } void doOmimGene(struct trackDb *tdb, char *item) /* Put up OmimGene track info. */ { genericHeader(tdb, item); printOmimGeneDetails(tdb, item, FALSE); printTrackHtml(tdb); } void printRgdSslpCustomUrl(struct trackDb *tdb, char *itemName, boolean encode) /* Print RGD QTL URL. */ { char *url = tdb->url; char *sslpId; char *chrom, *chromStart, *chromEnd; if (url != NULL && url[0] != 0) { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select id from rgdSslpLink where name='%s';", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { sslpId = row[0]; printf("<H2>Rat SSLP: %s</H2>", itemName); printf("<B>RGD SSLP Report: "); printf("<A HREF=\"%s%s\" target=_blank>", url, sslpId); printf("RGD:%s</B></A>\n", sslpId); } sqlFreeResult(&sr); sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from rgdSslp where name='%s';", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { chrom = row[0]; chromStart = row[1]; chromEnd = row[2]; printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } sqlFreeResult(&sr); hFreeConn(&conn); } } void doVax003Vax004(struct trackDb *tdb, char *item) /* Put up VAX 004 info. */ { char *id; struct sqlConnection *conn = hAllocConn(database); char *aliTbl = tdb->table; int start = cartInt(cart, "o"); char cond_str[255], *subjId; genericHeader(tdb, item); id = item; printf("<H3>Sequence ID: %s", id); printf("</H3>\n"); /* display subject ID */ sqlSafefFrag(cond_str, sizeof cond_str, "dnaSeqId='%s'", id); subjId = sqlGetField(database,"gsIdXref", "subjId", cond_str); printf("<H3>Subject ID: "); printf("<A HREF=\"../cgi-bin/gsidSubj?hgs_subj=%s\">", subjId); printf("%s</A>\n", subjId); printf("</H3>"); /* print alignments that track was based on */ struct psl *pslList = getAlignments(conn, aliTbl, item); printf("<H3>Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); hFreeConn(&conn); printTrackHtml(tdb); } void doUniGene3(struct trackDb *tdb, char *item) /* Put up UniGene info. */ { char *url = tdb->url; char *id; struct sqlConnection *conn = hAllocConn(database); char *aliTbl = tdb->table; int start = cartInt(cart, "o"); genericHeader(tdb, item); id = strstr(item, "Hs.")+strlen("Hs."); printf("<H3>%s UniGene: ", organism); printf("<A HREF=\"%s%s\" target=_blank>", url, id); printf("%s</B></A>\n", item); printf("</H3>\n"); /* print alignments that track was based on */ struct psl *pslList = getAlignments(conn, aliTbl, item); printf("<H3>Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); hFreeConn(&conn); printTrackHtml(tdb); } void doRgdSslp(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up Superfamily track info. */ { if (itemForUrl == NULL) itemForUrl = item; genericHeader(tdb, item); printRgdSslpCustomUrl(tdb, itemForUrl, item == itemForUrl); printTrackHtml(tdb); } static boolean isBDGPName(char *name) /* Return TRUE if name is from BDGP (matching {CG,TE,CR}0123{,4}{,-R?}) */ { int len = strlen(name); boolean isBDGP = FALSE; if (startsWith("CG", name) || startsWith("TE", name) || startsWith("CR", name)) { int numNum = 0; int i; for (i=2; i < len; i++) { if (isdigit(name[i])) numNum++; else break; } if ((numNum >= 4) && (numNum <= 5)) { if (i == len) isBDGP = TRUE; else if ((i == len-3) && (name[i] == '-') && (name[i+1] == 'R') && isalpha(name[i+2])) isBDGP = TRUE; } } return(isBDGP); } void doRgdGene(struct trackDb *tdb, char *rnaName) /* Process click on a RGD gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *sqlRnaName = rnaName; struct refLink *rl; char *rgdId; int start = cartInt(cart, "o"); /* Make sure to escape single quotes for DB parseability */ if (strchr(rnaName, '\'')) sqlRnaName = replaceChars(rnaName, "'", "''"); cartWebStart(cart, database, "%s", tdb->longLabel); sqlSafef(query, sizeof(query), "select * from %s where mrnaAcc = '%s'", refLinkTable, sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in %s table - this accession may no longer be available.", rnaName, refLinkTable); rl = refLinkLoad(row); sqlFreeResult(&sr); printf("<H2>Gene %s</H2>\n", rl->name); sqlSafef(query, sizeof(query), "select id from rgdGeneLink where refSeq = '%s'", sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in rgdGeneLink table - database inconsistency.", rnaName); rgdId = cloneString(row[0]); sqlFreeResult(&sr); printf("<B>RGD Gene Report: </B> <A HREF=\""); printf("%s%s", tdb->url, rgdId); printf("\" TARGET=_blank>RGD:%s</A><BR>", rgdId); printf("<B>NCBI RefSeq: </B> <A HREF=\""); printEntrezNucleotideUrl(stdout, rl->mrnaAcc); printf("\" TARGET=_blank>%s</A>", rl->mrnaAcc); /* If refSeqStatus is available, report it: */ if (sqlTableExists(conn, refSeqStatusTable)) { sqlSafef(query, sizeof(query), "select status from %s where mrnaAcc = '%s'", refSeqStatusTable, sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf(" Status: <B>%s</B>", row[0]); } sqlFreeResult(&sr); } puts("<BR>"); if (rl->omimId != 0) { printf("<B>OMIM:</B> <A HREF=\""); printEntrezOMIMUrl(stdout, rl->omimId); printf("\" TARGET=_blank>%d</A><BR>\n", rl->omimId); } if (rl->locusLinkId != 0) { printf("<B>Entrez Gene:</B> "); printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%d\" TARGET=_blank>", rl->locusLinkId); printf("%d</A><BR>\n", rl->locusLinkId); } htmlHorizontalLine(); /* print alignments that track was based on */ { char *aliTbl = (sameString(tdb->table, "rgdGene") ? "refSeqAli" : "xenoRGDAli"); struct psl *pslList = getAlignments(conn, aliTbl, rl->mrnaAcc); printf("<H3>mRNA/Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", aliTbl, rl->mrnaAcc); } htmlHorizontalLine(); geneShowPosAndLinks(rl->mrnaAcc, rl->protAcc, tdb, refPepTable, "htcTranslatedProtein", "htcRefMrna", "htcGeneInGenome", "mRNA Sequence"); printTrackHtml(tdb); hFreeConn(&conn); } void doRgdGene2(struct trackDb *tdb, char *rgdGeneId) /* Process click on a RGD gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *sqlRnaName = rgdGeneId; char *rgdId = NULL; char *chp; char *GeneID, *Name, *note; char *rgdPathwayName; /* Make sure to escape single quotes for DB parseability */ if (strchr(rgdGeneId, '\'')) sqlRnaName = replaceChars(rgdGeneId, "'", "''"); cartWebStart(cart, database, "%s", tdb->longLabel); chp = strstr(rgdGeneId, ":"); if (chp != NULL) { chp++; rgdId = strdup(chp); } else { errAbort("Couldn't find %s.", rgdGeneId); } sqlSafef(query, sizeof(query), "select GeneID, Name, note from rgdGeneXref where rgdGeneId = '%s'", sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in rgdGeneXref table - database inconsistency.", rgdGeneId); GeneID = cloneString(row[0]); Name = cloneString(row[1]); note = cloneString(row[2]); sqlFreeResult(&sr); printf("<H2>Gene %s</H2>\n", Name); printf("<B>RGD Gene Report: </B> <A HREF=\""); printf("%s%s", tdb->url, rgdId); printf("\" TARGET=_blank>RGD:%s</A>", rgdId); printf("<BR><B>GeneID: </B> %s ", GeneID); printf("<BR><B>Gene Name: </B> %s ", Name); printf("<BR><B>Note: </B> %s ", note); sqlSafef(query, sizeof(query), "select extAC from rgdGeneXref2 where rgdGeneId = '%s' and extDB='IMAGE'", rgdGeneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { char *image; image = cloneString(row[0]); printf("<BR><B>IMAGE Clone: </B>"); printf("<A HREF=\""); printf("%s%s", "http://www.imageconsortium.org/IQ/bin/singleCloneQuery?clone_id=", image); printf("\" TARGET=_blank> %s</A>", image); row = sqlNextRow(sr); while (row != NULL) { image = cloneString(row[0]); printf(", <A HREF=\""); printf("%s%s", "http://www.imageconsortium.org/IQ/bin/singleCloneQuery?clone_id=", image); printf("\" TARGET=_blank>%s</A>", image); row = sqlNextRow(sr); } } sqlFreeResult(&sr); sqlSafef(query, sizeof(query), "select extAC from rgdGeneXref2 where rgdGeneId = '%s' and extDB='MGC'", rgdGeneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { char *mgc; mgc = cloneString(row[0]); printf("<BR><B>MGC: </B>"); printf("<A HREF=\""); printf("%s%s", "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Rn&LIST=", mgc); printf("\" TARGET=_blank> %s</A>", mgc); row = sqlNextRow(sr); while (row != NULL) { mgc = cloneString(row[0]); printf(", <A HREF=\""); printf("%s%s", "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Rn&LIST=", mgc); printf("\" TARGET=_blank>%s</A>", mgc); row = sqlNextRow(sr); } } sqlFreeResult(&sr); htmlHorizontalLine(); printf("<H3>RGD Pathway(s)</H3>\n"); sqlSafef(query, sizeof(query), "select p.rgdPathwayId, p.name from rgdGenePathway g, rgdPathway p where g.rgdGeneId = '%s' and g.rgdPathwayId=p.rgdPathwayId", rgdGeneId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in rgdGenePathway table - database inconsistency.", rgdGeneId); printf("<UL>"); while (row != NULL) { rgdPathwayName = cloneString(row[1]); printf("<LI><B>%s</B><BR>", rgdPathwayName); row = sqlNextRow(sr); } sqlFreeResult(&sr); printf("</UL>"); printf("<A HREF=\""); printf("%s%s%s", "http://rgd.mcw.edu/tools/genes/gene_ont_view.cgi?id=", rgdId, "#Pathway"); printf("\" TARGET=_blank> %s</A> </H3>", "Click here for more RGD pathway details related to this gene..."); htmlHorizontalLine(); printTrackHtml(tdb); hFreeConn(&conn); } char *getRefSeqCdsCompleteness(struct sqlConnection *conn, char *acc) /* get description of RefSeq CDS completeness or NULL if not available */ { /* table mapping names to descriptions */ static char *cmplMap[][2] = { {"Unknown", "completeness unknown"}, {"Complete5End", "5' complete"}, {"Complete3End", "3' complete"}, {"FullLength", "full length"}, {"IncompleteBothEnds", "5' and 3' incomplete"}, {"Incomplete5End", "5' incomplete"}, {"Incomplete3End", "3' incomplete"}, {"Partial", "partial"}, {NULL, NULL} }; if (sqlTableExists(conn, refSeqSummaryTable)) { char query[256], buf[64], *cmpl; int i; sqlSafef(query, sizeof(query), "select completeness from %s where mrnaAcc = '%s'", refSeqSummaryTable, acc); cmpl = sqlQuickQuery(conn, query, buf, sizeof(buf)); if (cmpl != NULL) { for (i = 0; cmplMap[i][0] != NULL; i++) { if (sameString(cmpl, cmplMap[i][0])) return cmplMap[i][1]; } } } return NULL; } char *getRefSeqSummary(struct sqlConnection *conn, char *acc) /* RefSeq summary or NULL if not available; free result */ { char * summary = NULL; if (sqlTableExists(conn, refSeqSummaryTable)) { char query[256]; sqlSafef(query, sizeof(query), "select summary from %s where mrnaAcc = '%s'", refSeqSummaryTable, acc); summary = sqlQuickString(conn, query); } return summary; } char *geneExtraImage(char *geneFileBase) /* check if there is a geneExtra image for the specified gene, if so return * the relative URL in a static buffer, or NULL if it doesn't exist */ { static char *imgExt[] = {"png", "gif", "jpg", NULL}; static char path[256]; int i; for (i = 0; imgExt[i] != NULL; i++) { safef(path, sizeof(path), "../htdocs/geneExtra/%s.%s", geneFileBase, imgExt[i]); if (access(path, R_OK) == 0) { safef(path, sizeof(path), "../geneExtra/%s.%s", geneFileBase, imgExt[i]); return path; } } return NULL; } void addGeneExtra(char *geneName) /* create html table columns with geneExtra data, see hgdocs/geneExtra/README * for details */ { char geneFileBase[256], *imgPath, textPath[256]; /* lower-case gene name used as key */ safef(geneFileBase, sizeof(geneFileBase), "%s", geneName); tolowers(geneFileBase); /* add image column, if exists */ imgPath = geneExtraImage(geneFileBase); if (imgPath != NULL) printf("<td><img src=\"%s\">", imgPath); /* add text column, if exists */ safef(textPath, sizeof(textPath), "../htdocs/geneExtra/%s.txt", geneFileBase); if (access(textPath, R_OK) == 0) { FILE *fh = mustOpen(textPath, "r"); printf("<td valign=\"center\">"); copyOpenFile(fh, stdout); fclose(fh); } } int gbCdnaGetVersion(struct sqlConnection *conn, char *acc) /* return mrna/est version, or 0 if not available */ { int ver = 0; if (!sqlTableExists(conn, gbCdnaInfoTable)) { warn("Genbank information not shown below, the table %s is not installed " "on this server. ", gbCdnaInfoTable); //"The information below is a shortened version of the one shown on the " //"<a href=\"http://genome.ucsc.edu\">UCSC site</a>", database); return 0; } if (hHasField(database, gbCdnaInfoTable, "version")) { char query[128]; sqlSafef(query, sizeof(query), "select version from %s where acc = '%s'", gbCdnaInfoTable, acc); ver = sqlQuickNum(conn, query); } return ver; } static void prRefGeneXenoInfo(struct sqlConnection *conn, struct refLink *rl) /* print xeno refseq info, including linking to the browser, if any */ { char query[256]; sqlSafef(query, sizeof(query), "select o.name from %s g,%s o " "where (g.acc = '%s') and (o.id = g.organism)", gbCdnaInfoTable, organismTable, rl->mrnaAcc); char *org = sqlQuickString(conn, query); if (org == NULL) org = cloneString("unknown"); printf("<B>Organism:</B> %s<BR>", org); char *xenoDb = hDbForSciName(org); if ((xenoDb != NULL) && hDbIsActive(xenoDb) && hTableExists(xenoDb, "refSeqAli")) { printf("<B>UCSC browser: </B> \n"); linkToOtherBrowserSearch(xenoDb, rl->mrnaAcc); printf("%s on %s (%s)</B> \n", rl->mrnaAcc, hOrganism(xenoDb), xenoDb); printf("</A><BR>"); } freeMem(org); } void prRefGeneInfo(struct sqlConnection *conn, char *rnaName, char *sqlRnaName, struct refLink *rl, boolean isXeno) /* print basic details information and links for a RefGene */ { struct sqlResult *sr; char **row; char query[256]; int ver = gbCdnaGetVersion(conn, rl->mrnaAcc); char *cdsCmpl = NULL; printf("<td valign=top nowrap>\n"); if (isXeno) { if (startsWith("panTro", database)) printf("<H2>Other RefSeq Gene %s</H2>\n", rl->name); else printf("<H2>Non-%s RefSeq Gene %s</H2>\n", organism, rl->name); } else printf("<H2>RefSeq Gene %s</H2>\n", rl->name); printf("<B>RefSeq:</B> <A HREF=\""); printEntrezNucleotideUrl(stdout, rl->mrnaAcc); if (ver > 0) printf("\" TARGET=_blank>%s.%d</A>", rl->mrnaAcc, ver); else printf("\" TARGET=_blank>%s</A>", rl->mrnaAcc); /* If refSeqStatus is available, report it: */ if (sqlTableExists(conn, refSeqStatusTable)) { sqlSafef(query, sizeof(query), "select status from %s where mrnaAcc = '%s'", refSeqStatusTable, sqlRnaName); char *stat = sqlQuickString(conn, query); if (stat != NULL) printf(" <B>Status: </B>%s", stat); } puts("<BR>"); char *desc = gbCdnaGetDescription(conn, rl->mrnaAcc); if (desc != NULL) { printf("<B>Description:</B> "); htmlTextOut(desc); printf("<BR>\n"); } if (isXeno) prRefGeneXenoInfo(conn, rl); else printCcdsForSrcDb(conn, rl->mrnaAcc); cdsCmpl = getRefSeqCdsCompleteness(conn, sqlRnaName); if (cdsCmpl != NULL) { printf("<B>CDS:</B> %s<BR>", cdsCmpl); } if (rl->omimId != 0) { printf("<B>OMIM:</B> <A HREF=\""); printEntrezOMIMUrl(stdout, rl->omimId); printf("\" TARGET=_blank>%d</A><BR>\n", rl->omimId); } if (rl->locusLinkId != 0) { printf("<B>Entrez Gene:</B> "); printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%d\" TARGET=_blank>", rl->locusLinkId); printf("%d</A><BR>\n", rl->locusLinkId); if ( (strstr(database, "mm") != NULL) && hTableExists(database, "MGIid")) { char *mgiID; sqlSafef(query, sizeof(query), "select MGIid from MGIid where LLid = '%d';", rl->locusLinkId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Mouse Genome Informatics:</B> "); mgiID = cloneString(row[0]); printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); } else { /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree * with Locuslink on seq to gene association. * Thus, not finding a MGIid even if a LocusLink ID * exists is always a possibility. */ } sqlFreeResult(&sr); } } if (!startsWith("Worm", organism)) { if (startsWith("dm", database)) { /* PubMed never seems to have BDGP gene IDs... so if that's all * that's given for a name/product, ignore name / truncate product. */ char *cgp = strstr(rl->product, "CG"); if (cgp != NULL) { char *cgWord = firstWordInLine(cloneString(cgp)); char *dashp = strchr(cgWord, '-'); if (dashp != NULL) *dashp = 0; if (isBDGPName(cgWord)) *cgp = 0; } if (! isBDGPName(rl->name)) medlineLinkedLine("PubMed on Gene", rl->name, rl->name); if (rl->product[0] != 0) medlineProductLinkedLine("PubMed on Product", rl->product); } else { medlineLinkedLine("PubMed on Gene", rl->name, rl->name); if (rl->product[0] != 0) medlineProductLinkedLine("PubMed on Product", rl->product); } printf("\n"); printGeneCards(rl->name); } if (hTableExists(database, "jaxOrtholog")) { struct jaxOrtholog jo; char * sqlRlName = rl->name; /* Make sure to escape single quotes for DB parseability */ if (strchr(rl->name, '\'')) { sqlRlName = replaceChars(rl->name, "'", "''"); } sqlSafef(query, sizeof(query), "select * from jaxOrtholog where humanSymbol='%s'", sqlRlName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { jaxOrthologStaticLoad(row, &jo); printf("<B>MGI Mouse Ortholog:</B> "); printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" target=_BLANK>", jo.mgiId); printf("%s</A><BR>\n", jo.mouseSymbol); } sqlFreeResult(&sr); } if (startsWith("hg", database)) { printf("\n"); printf("<B>AceView:</B> "); printf("<A HREF = \"https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s\" TARGET=_blank>", rl->name); printf("%s</A><BR>\n", rl->name); } prGRShortRefGene(rl->name); } void prKnownGeneInfo(struct sqlConnection *conn, char *rnaName, char *sqlRnaName, struct refLink *rl) /* print basic details information and links for a Known Gene */ { struct sqlResult *sr; char **row; char query[256]; int ver = gbCdnaGetVersion(conn, rl->mrnaAcc); char *cdsCmpl = NULL; printf("<td valign=top nowrap>\n"); printf("<H2>Known Gene %s</H2>\n", rl->name); printf("<B>KnownGene:</B> <A HREF=\""); printEntrezNucleotideUrl(stdout, rl->mrnaAcc); if (ver > 0) printf("\" TARGET=_blank>%s.%d</A>", rl->mrnaAcc, ver); else printf("\" TARGET=_blank>%s</A>", rl->mrnaAcc); fflush(stdout); puts("<BR>"); char *desc = gbCdnaGetDescription(conn, rl->mrnaAcc); if (desc != NULL) { printf("<B>Description:</B> "); htmlTextOut(desc); printf("<BR>\n"); } printCcdsForSrcDb(conn, rl->mrnaAcc); cdsCmpl = getRefSeqCdsCompleteness(conn, sqlRnaName); if (cdsCmpl != NULL) { printf("<B>CDS:</B> %s<BR>", cdsCmpl); } if (rl->omimId != 0) { printf("<B>OMIM:</B> <A HREF=\""); printEntrezOMIMUrl(stdout, rl->omimId); printf("\" TARGET=_blank>%d</A><BR>\n", rl->omimId); } if (rl->locusLinkId != 0) { printf("<B>Entrez Gene:</B> "); printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%d\" TARGET=_blank>", rl->locusLinkId); printf("%d</A><BR>\n", rl->locusLinkId); if ( (strstr(database, "mm") != NULL) && hTableExists(database, "MGIid")) { char *mgiID; sqlSafef(query, sizeof(query), "select MGIid from MGIid where LLid = '%d';", rl->locusLinkId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Mouse Genome Informatics:</B> "); mgiID = cloneString(row[0]); printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); } else { /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree * with Locuslink on seq to gene association. * Thus, not finding a MGIid even if a LocusLink ID * exists is always a possibility. */ } sqlFreeResult(&sr); } } } void doKnownGene(struct trackDb *tdb, char *rnaName) /* Process click on a known gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *kgId = cartString(cart, "i"); char *sqlRnaName = rnaName; char *summary = NULL; struct refLink rlR; struct refLink *rl; int start = cartInt(cart, "o"); int left = cartInt(cart, "l"); int right = cartInt(cart, "r"); char *chrom = cartString(cart, "c"); /* Make sure to escape single quotes for DB parseability */ if (strchr(rnaName, '\'')) { sqlRnaName = replaceChars(rnaName, "'", "''"); } /* get refLink entry */ if (strstr(rnaName, "NM_") != NULL) { sqlSafef(query, sizeof(query), "select * from %s where mrnaAcc = '%s'", refLinkTable, sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in %s table - this accession may no longer be available.", rnaName, refLinkTable); rl = refLinkLoad(row); sqlFreeResult(&sr); } else { rlR.name = strdup(kgId); rlR.mrnaAcc = strdup(kgId); rlR.locusLinkId = 0; rl = &rlR; } cartWebStart(cart, database, "Known Gene"); printf("<table border=0>\n<tr>\n"); prKnownGeneInfo(conn, rnaName, sqlRnaName, rl); printf("</tr>\n</table>\n"); /* optional summary text */ summary = getRefSeqSummary(conn, kgId); if (summary != NULL) { htmlHorizontalLine(); printf("<H3>Summary of %s</H3>\n", kgId); printf("<P>%s</P>\n", summary); freeMem(summary); } htmlHorizontalLine(); /* print alignments that track was based on */ { char *aliTbl; if (strstr(kgId, "NM_")) { aliTbl = strdup("refSeqAli"); } else { aliTbl = strdup("all_mrna"); } struct psl *pslList = getAlignments(conn, aliTbl, rl->mrnaAcc); printf("<H3>mRNA/Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", aliTbl, kgId); } htmlHorizontalLine(); struct palInfo *palInfo = NULL; if (genbankIsRefSeqCodingMRnaAcc(rnaName)) { AllocVar(palInfo); palInfo->chrom = chrom; palInfo->left = left; palInfo->right = right; palInfo->rnaName = rnaName; } geneShowPosAndLinksPal(rl->mrnaAcc, rl->protAcc, tdb, refPepTable, "htcTranslatedProtein", "htcRefMrna", "htcGeneInGenome", "mRNA Sequence",palInfo); printTrackHtml(tdb); hFreeConn(&conn); } static struct refLink *printRefSeqInfo( struct sqlConnection *conn, struct trackDb *tdb, char *rnaName, char *version) { struct sqlResult *sr; char **row; char query[256]; char *sqlRnaName = rnaName; char *summary = NULL; boolean isXeno = sameString(tdb->table, "xenoRefGene"); struct refLink *rl; /* Make sure to escape single quotes for DB parseability */ if (strchr(rnaName, '\'')) { sqlRnaName = replaceChars(rnaName, "'", "''"); } /* get refLink entry */ if (version == NULL) { sqlSafef(query, sizeof(query), "select * from %s where mrnaAcc = '%s'", refLinkTable, sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("This accession (%s) is no longer in our database. Check NCBI for status on this accession.", rnaName); rl = refLinkLoad(row); sqlFreeResult(&sr); } else { sqlSafef(query, sizeof(query), "select * from %s r, %s g where mrnaAcc = '%s' and r.mrnaAcc=g.acc and g.version='%s'", refLinkTable,gbCdnaInfoTable, sqlRnaName, version); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) { sqlFreeResult(&sr); return NULL; } rl = refLinkLoad(row); sqlFreeResult(&sr); } /* print the first section with info */ printf("<table border=0>\n<tr>\n"); prRefGeneInfo(conn, rnaName, sqlRnaName, rl, isXeno); addGeneExtra(rl->name); /* adds columns if extra info is available */ printf("</tr>\n</table>\n"); /* optional summary text */ summary = getRefSeqSummary(conn, sqlRnaName); if (summary != NULL) { htmlHorizontalLine(); printf("<H3>Summary of %s</H3>\n", rl->name); printf("<P>%s</P>\n", summary); freeMem(summary); } htmlHorizontalLine(); return rl; } void doNcbiRefSeq(struct trackDb *tdb, char *itemName) /* Process click on a NCBI RefSeq gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; struct ncbiRefSeqLink *nrl; cartWebStart(cart, database, "%s - %s ", tdb->longLabel, itemName); /* get refLink entry */ sqlSafef(query, sizeof(query), "select * from ncbiRefSeqLink where id = '%s'", itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in ncbiRefSeqLink table.", itemName); nrl = ncbiRefSeqLinkLoad(row); sqlFreeResult(&sr); printf("<h2>RefSeq Gene %s</h2><br>\n", nrl->name); printf("<b>RefSeq:</b> <a href='"); printEntrezNucleotideUrl(stdout, nrl->id); printf("' target=_blank>%s</a>", nrl->id); printf(" <b>Status: </b>%s<br>\n", nrl->status); printf("<b>Description:</b> %s<br>\n", nrl->product); if (differentWord(nrl->gbkey, "")) { printf("<b>Molecule type:</b> %s<br>\n", nrl->gbkey); } if (differentWord(nrl->pseudo, "")) { printf("<b>Pseudogene:</b> %s<br>\n", nrl->pseudo); } if (differentWord(nrl->source, "")) { printf("<b>Source:</b> %s<br>\n", nrl->source); } if (differentWord(nrl->gene_biotype, "")) { printf("<b>Biotype:</b> %s<br>\n", nrl->gene_biotype); } if (differentWord(nrl->gene_synonym, "")) { printf("<b>Synonyms:</b> %s<br>\n", nrl->gene_synonym); } if (differentWord(nrl->ncrna_class, "")) { printf("<b>ncRNA class:</b> %s<br>\n", nrl->ncrna_class); } if (differentWord(nrl->note, "")) { printf("<b>Other notes:</b> %s<br>\n", nrl->note); } if (differentWord(nrl->omimId, "")) { printf("<b>OMIM:</b> <a href='"); printEntrezOMIMUrl(stdout, sqlSigned(nrl->omimId)); printf("' target=_blank>%s</a><br>\n", nrl->omimId); } if (differentWord(nrl->mrnaAcc, "") && differentWord(nrl->mrnaAcc,nrl->id)) { printf("<b>mRNA:</b> "); printf("<a href='https://www.ncbi.nlm.nih.gov/nuccore/%s' target=_blank>", nrl->mrnaAcc); printf("%s</a><br>\n", nrl->mrnaAcc); } if (differentWord(nrl->genbank, "") && differentWord(nrl->genbank,nrl->id)) { printf("<b>Genbank:</b> "); printf("<a href='https://www.ncbi.nlm.nih.gov/nuccore/%s' target=_blank>", nrl->genbank); printf("%s</a><br>\n", nrl->genbank); } if (differentWord(nrl->protAcc, "")) { printf("<b>Protein:</b> "); printf("<a href='https://www.ncbi.nlm.nih.gov/protein/%s' target=_blank>", nrl->protAcc); printf("%s</a><br>\n", nrl->protAcc); } if (differentWord(nrl->hgnc, "")) { /* legacy support of mm10 override of hgnc column until this table * is updated on the RR */ if (startsWith("MGI", nrl->hgnc)) { printf("<b>MGI:</b> " "<a href=\"http://www.informatics.jax.org/marker/%s\" target=_blank>%s</a><br>\n", nrl->hgnc, nrl->hgnc); } else { printf("<b>HGNC:</b> "); printf("<a href='http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:%s' target=_blank>", nrl->hgnc); printf("%s</a><br>\n", nrl->hgnc); } } if (sqlColumnExists(conn, "ncbiRefSeqLink", "externalId")) { if (differentWord(nrl->externalId, "")) { char *urlsStr = trackDbSetting(tdb, "dbPrefixUrls"); struct hash* dbToUrl = hashFromString(urlsStr); char *labelsStr = trackDbSetting(tdb, "dbPrefixLabels"); struct hash* dbToLabel = hashFromString(labelsStr); if (dbToUrl) { if (!dbToLabel) errAbort("can not find trackDb dbPrefixLabels to correspond with dbPrefixUrls\n"); char *databasePrefix = cloneString(database); while (strlen(databasePrefix) && isdigit(lastChar(databasePrefix))) trimLastChar(databasePrefix); struct hashEl *hel = hashLookup(dbToUrl, databasePrefix); if (hel) { struct hashEl *label = hashLookup(dbToLabel, databasePrefix); if (!label) errAbort("missing trackDb dbPrefixLabels for database prefix: '%s'\n", databasePrefix); char *url = (char *)hel->val; char *labelStr = (char *)label->val; char *idUrl = replaceInUrl(url, nrl->externalId, cart, database, nrl->externalId, winStart, winEnd, tdb->track, TRUE, NULL); printf("<b>%s:</b> ", labelStr); printf("<a href='%s' target='_blank'>%s</a><br>\n", idUrl, nrl->externalId); } } } } if (differentWord(nrl->locusLinkId, "")) { printf("<b>Entrez Gene:</b> "); printf("<a href='https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' TARGET=_blank>", nrl->locusLinkId); printf("%s</a><br>\n", nrl->locusLinkId); } if (differentWord(nrl->name,"")) { printGeneCards(nrl->name); if (startsWith("hg", database)) { printf("<b>AceView:</b> "); printf("<a href = 'https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s' target=_blank>", nrl->name); printf("%s</a><br>\n", nrl->name); } } htmlHorizontalLine(); if (differentWord("", nrl->description)) { printf("Summary of <b>%s</b><br>\n%s<br>\n", nrl->name, nrl->description); htmlHorizontalLine(); } static boolean hasSequence = TRUE; struct psl *pslList = getAlignments(conn, "ncbiRefSeqPsl", itemName); // if the itemName isn't found, it might be found as the nrl->mrnaAcc if (! pslList) pslList = getAlignments(conn, "ncbiRefSeqPsl", nrl->mrnaAcc); if (pslList) { char query[256]; /* verify itemName has RNA sequence to work with */ sqlSafef(query, sizeof(query), "select id from seqNcbiRefSeq where acc='%s' limit 1", itemName); char * result= sqlQuickString(conn, query); if (isEmpty(result)) { printf ("<h4>No sequence available for %s, can't display alignment.</h4>\n", itemName); hasSequence = FALSE; } else { printf("<H3>mRNA/Genomic Alignments (%s)</H3>", itemName); int start = cartInt(cart, "o"); printAlignments(pslList, start, "htcCdnaAli", "ncbiRefSeqPsl", itemName); } } else { printf ("<h4>Missing alignment for %s</h4><br>\n", itemName); } htmlHorizontalLine(); if (! ( sameString(tdb->track, "ncbiRefSeqPsl") || sameString(tdb->track, "ncbiRefSeqOther" ) ) ) showGenePos(itemName, tdb); printf("<h3>Links to sequence:</h3>\n"); printf("<ul>\n"); if (differentWord("", nrl->protAcc)) { puts("<li>\n"); hgcAnchorSomewhere("htcTranslatedProtein", nrl->protAcc, "ncbiRefSeqPepTable", seqName); printf("Predicted Protein</a> \n"); puts("</li>\n"); } if (hasSequence) { puts("<li>\n"); hgcAnchorSomewhere("ncbiRefSeqSequence", itemName, "ncbiRefSeqPsl", seqName); printf("%s</a> may be different from the genomic sequence.\n", "Predicted mRNA"); puts("</li>\n"); } puts("<LI>\n"); hgcAnchorSomewhere("getDna", itemName, tdb->track, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); printf("</ul>\n"); printTrackHtml(tdb); hFreeConn(&conn); } void doRefGene(struct trackDb *tdb, char *rnaName) /* Process click on a known RefSeq gene. */ { struct sqlConnection *conn = hAllocConn(database); int start = cartInt(cart, "o"); int left = cartInt(cart, "l"); int right = cartInt(cart, "r"); char *chrom = cartString(cart, "c"); boolean isXeno = sameString(tdb->table, "xenoRefGene"); if (isXeno) cartWebStart(cart, database, "Non-%s RefSeq Gene", organism); else cartWebStart(cart, database, "RefSeq Gene"); struct refLink *rl = printRefSeqInfo( conn, tdb, rnaName, NULL); /* print alignments that track was based on */ char *aliTbl = (sameString(tdb->table, "refGene") ? "refSeqAli" : "xenoRefSeqAli"); if (hTableExists(database, aliTbl)) { struct psl *pslList = getAlignments(conn, aliTbl, rl->mrnaAcc); printf("<H3>mRNA/Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", aliTbl, rl->mrnaAcc); } else warn("Sequence alignment links not shown below, the table %s.refSeqAli is not installed " "on this server", database); htmlHorizontalLine(); struct palInfo *palInfo = NULL; if (genbankIsRefSeqCodingMRnaAcc(rnaName)) { AllocVar(palInfo); palInfo->chrom = chrom; palInfo->left = left; palInfo->right = right; palInfo->rnaName = rnaName; } geneShowPosAndLinksPal(rl->mrnaAcc, rl->protAcc, tdb, refPepTable, "htcTranslatedProtein", "htcRefMrna", "htcGeneInGenome", "mRNA Sequence",palInfo); printTrackHtml(tdb); hFreeConn(&conn); } char *kgIdToSpId(struct sqlConnection *conn, char* kgId) /* get the swissprot id for a known genes id; resulting string should be * freed */ { char query[512]; sqlSafef(query, sizeof(query), "select spID from kgXref where kgID='%s'", kgId); return sqlNeedQuickString(conn, query); } void doHInvGenes(struct trackDb *tdb, char *item) /* Process click on H-Invitational genes track. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; int start = cartInt(cart, "o"); struct psl *pslList = NULL; struct HInv *hinv; /* Print non-sequence info. */ genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select * from HInv where geneId = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hinv = HInvLoad(row); if (hinv != NULL) { printf("<B> Gene ID: </B> <A HREF=\"http://www.jbirc.jbic.or.jp/hinv/soup/pub_Detail.pl?acc_id=%s\" TARGET=_blank> %s <BR></A>", hinv->mrnaAcc, hinv->geneId ); printf("<B> Cluster ID: </B> <A HREF=\"http://www.jbirc.jbic.or.jp/hinv/soup/pub_Locus.pl?locus_id=%s\" TARGET=_blank> %s <BR></A>", hinv->clusterId, hinv->clusterId ); printf("<B> cDNA Accession: </B> <A HREF=\"http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry.pl?%s\" TARGET=_blank> %s <BR></A>", hinv->mrnaAcc, hinv->mrnaAcc ); } } htmlHorizontalLine(); /* print alignments that track was based on */ pslList = getAlignments(conn, "HInvGeneMrna", item); puts("<H3>mRNA/Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", "HInvGeneMrna", item); printTrackHtml(tdb); hFreeConn(&conn); } char *getGi(char *ncbiFaHead) /* Get GI number from NCBI FA format header. */ { char *s; static char gi[64]; if (!startsWith("gi|", ncbiFaHead)) return NULL; ncbiFaHead += 3; strncpy(gi, ncbiFaHead, sizeof(gi)); s = strchr(gi, '|'); if (s != NULL) *s = 0; return trimSpaces(gi); } void showSAM_T02(char *itemName) { char query2[256]; struct sqlResult *sr2; char **row2; struct sqlConnection *conn2 = hAllocConn(database); char cond_str[256]; char *predFN; char *homologID; char *SCOPdomain; char *chain; char goodSCOPdomain[40]; int first = 1; float eValue; char *chp; int homologCount; int gotPDBFile; printf("<B>Protein Structure Analysis and Prediction by "); printf("<A HREF=\"http://www.soe.ucsc.edu/research/compbio/SAM_T02/sam-t02-faq.html\""); printf(" TARGET=_blank>SAM-T02</A></B><BR><BR>\n"); printf("<B>Multiple Alignment:</B> "); /* printf("<A HREF=\"http://www.soe.ucsc.edu/~karplus/SARS/%s/summary.html#alignment", */ printf("<A HREF=\"../SARS/%s/summary.html#alignment", itemName); printf("\" TARGET=_blank>%s</A><BR>\n", itemName); printf("<B>Secondary Structure Predictions:</B> "); /* printf("<A HREF=\"http://www.soe.ucsc.edu/~karplus/SARS/%s/summary.html#secondary-structure", */ printf("<A HREF=\"../SARS/%s/summary.html#secondary-structure", itemName); printf("\" TARGET=_blank>%s</A><BR>\n", itemName); printf("<B>3D Structure Prediction (PDB file):</B> "); gotPDBFile = 0; sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s' and evalue <1.0e-5;", itemName); if (sqlGetField(database, "protHomolog", "proteinID", cond_str) != NULL) { sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s'", itemName); predFN = sqlGetField(database, "protPredFile", "predFileName", cond_str); if (predFN != NULL) { printf("<A HREF=\"../SARS/%s/", itemName); /* printf("%s.t2k.undertaker-align.pdb\">%s</A><BR>\n", itemName,itemName); */ printf("%s\">%s</A><BR>\n", predFN,itemName); gotPDBFile = 1; } } if (!gotPDBFile) { printf("No high confidence level structure prediction available for this sequence."); printf("<BR>\n"); } printf("<B>3D Structure of Close Homologs:</B> "); homologCount = 0; strcpy(goodSCOPdomain, "dummy"); conn2= hAllocConn(database); sqlSafef(query2, sizeof(query2), "select homologID,eValue,SCOPdomain,chain from sc1.protHomolog where proteinID='%s' and evalue <= 0.01;", itemName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { while (row2 != NULL) { homologID = row2[0]; sscanf(row2[1], "%e", &eValue); SCOPdomain = row2[2]; chp = SCOPdomain+strlen(SCOPdomain)-1; while (*chp != '.') chp--; *chp = '\0'; chain = row2[3]; if (eValue <= 1.0e-10) strcpy(goodSCOPdomain, SCOPdomain); else { if (strcmp(goodSCOPdomain,SCOPdomain) != 0) goto skip; else if (eValue > 0.1) goto skip; } if (first) first = 0; else printf(", "); printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=%s", homologID); if (strlen(chain) >= 1) printf("\"TARGET=_blank>%s(chain %s)</A>", homologID, chain); else printf("\"TARGET=_blank>%s</A>", homologID); homologCount++; skip: row2 = sqlNextRow(sr2); } } hFreeConn(&conn2); sqlFreeResult(&sr2); if (homologCount == 0) printf("None<BR>\n"); printf("<BR><B>Details:</B> "); printf("<A HREF=\"../SARS/%s/summary.html", itemName); printf("\" TARGET=_blank>%s</A><BR>\n", itemName); htmlHorizontalLine(); } void showHomologies(char *geneName, char *table) /* Show homology info. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; boolean isFirst = TRUE, gotAny = FALSE; char *gi; struct softberryHom hom; if (sqlTableExists(conn, table)) { sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, geneName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { softberryHomStaticLoad(row, &hom); if ((gi = getGi(hom.giString)) == NULL) continue; if (isFirst) { htmlHorizontalLine(); printf("<H3>Protein Homologies:</H3>\n"); isFirst = FALSE; gotAny = TRUE; } printf("<A HREF=\""); char temp[256]; safef(temp, sizeof(temp), "%s", gi); printEntrezProteinUrl(stdout, temp); printf("\" TARGET=_blank>%s</A> %s<BR>", hom.giString, hom.description); } } if (gotAny) htmlHorizontalLine(); hFreeConn(&conn); } void showPseudoHomologies(char *geneName, char *table) /* Show homology info. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; boolean isFirst = TRUE, gotAny = FALSE; struct borkPseudoHom hom; char *parts[10]; int partCount; char *clone; if (sqlTableExists(conn, table)) { sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, geneName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { borkPseudoHomStaticLoad(row, &hom); /* if ((gi = getGi(hom.giString)) == NULL) * continue; */ if (isFirst) { htmlHorizontalLine(); printf("<H3>Aligning Protein :</H3>\n"); isFirst = FALSE; gotAny = TRUE; } clone = cloneStringZ(hom.protRef,80); partCount = chopString(hom.protRef, "_", parts, ArraySize(parts)); if (partCount > 1) { printf("<A HREF="); char temp[256]; safef(temp, sizeof(temp), "%s", parts[1]); printSwissProtProteinUrl(stdout, temp); printf(" TARGET=_blank>Jump to SwissProt %s </A> " ,geneName); } printf(" %s <BR><BR>Alignment Information:<BR><BR>%s<BR>", clone, hom.description); } } if (gotAny) htmlHorizontalLine(); hFreeConn(&conn); } void pseudoPrintPosHeader(struct bed *bed) /* print header of pseudogene record */ { printf("<p>"); printf("<B>%s PseudoGene:</B> %s:%d-%d %d bp<BR>\n", hOrganism(database), bed->chrom, bed->chromStart, bed->chromEnd, bed->chromEnd-bed->chromStart); printf("Strand: %c",bed->strand[0]); printf("<p>"); } void pseudoPrintPos(struct psl *pseudoList, struct pseudoGeneLink *pg, char *alignTable, int start, char *acc) /* print details of pseudogene record */ { char query[256]; struct dyString *dy = newDyString(1024); char pfamDesc[128], *pdb; char chainTable[64]; char chainTable_chrom[64]; struct sqlResult *sr; char **row; struct sqlConnection *conn = hAllocConn(database); int first = 0; safef(chainTable,sizeof(chainTable), "selfChain"); if (!hTableExists(database, chainTable) ) safef(chainTable,sizeof(chainTable), "chainSelf"); printf("<B>Description:</B> Retrogenes are processed mRNAs that are inserted back into the genome. Most are pseudogenes, and some are functional genes or anti-sense transcripts that may impede mRNA translation.<p>\n"); printf("<B>Percent of retro that breaks net relative to Mouse : </B>%d %%<br>\n",pg->overlapMouse); printf("<B>Percent of retro that breaks net relative to Dog : </B>%d %%<br>\n",pg->overlapDog); printf("<B>Percent of retro that breaks net relative to Macaque : </B>%d %%<br>\n",pg->overlapRhesus); printf("<B>Exons Inserted:</B> %d out of %d %d Parent Splice Sites <br>\n",pg->exonCover - pg->conservedSpliceSites, pg->exonCover,pg->exonCount); printf("<B>Conserved Splice Sites:</B> %d <br>\n",pg->conservedSpliceSites); printf("<B>PolyA tail:</B> %d As out of %d bp <B>PolyA Percent Id: </B>%5.1f %%\n",pg->polyA,pg->polyAlen, (float)pg->polyA*100/(float)pg->polyAlen); printf(" (%d bp from end of retrogene)<br>\n",pg->polyAstart); printf("<B>Bases matching:</B> %d \n", pg->matches); printf("(%d %% of gene)<br>\n",pg->coverage); if (!sameString(pg->overName, "none")) printf("<B>Bases overlapping mRNA:</B> %s (%d bp)<br>\n", pg->overName, pg->maxOverlap); else printf("<B>No overlapping mRNA</B><br>"); if (sameString(pg->type, "singleExon")) printf("<b>Overlap with Parent: </b>%s<p>\n",pg->type); else printf("<b>Type of RetroGene: </b>%s<p>\n",pg->type); if (pseudoList != NULL) { printf("<H4>RetroGene/Gene Alignment</H4>"); printAlignments(pseudoList, start, "htcCdnaAli", alignTable, acc); } printf("<H4>Annotation for Gene locus that spawned RetroGene</H4>"); printf("<ul>"); if (!sameString(pg->refSeq,"noRefSeq")) { printf("<LI><B>RefSeq:</B> %s \n", pg->refSeq); linkToOtherBrowserExtra(database, pg->gChrom, pg->rStart, pg->rEnd, "refGene=pack"); printf("%s:%d-%d \n", pg->gChrom, pg->rStart, pg->rEnd); printf("</A></LI>"); } if (!sameString(pg->kgName,"noKg")) { printf("<LI><B>KnownGene:</B> " ); printf("<A TARGET=\"_blank\" "); printf("HREF=\"../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d\" ", cartSidUrlString(cart), "db", database, "hgg_gene", pg->kgName, "hgg_chrom", pg->gChrom, "hgg_start", pg->kStart, "hgg_end", pg->kEnd); printf(">%s</A> ",pg->kgName); linkToOtherBrowserExtra(database, pg->gChrom, pg->kStart, pg->kEnd, "knownGene=pack"); printf("%s:%d-%d \n", pg->gChrom, pg->kStart, pg->kEnd); printf("</A></LI>"); if (hTableExists(database, "knownGene")) { char *description; sqlSafef(query, sizeof(query), "select proteinId from knownGene where name = '%s'", pg->kgName); description = sqlQuickString(conn, query); if (description != NULL) { printf("<LI><B>SwissProt ID: </B> " ); printf("<A TARGET=\"_blank\" HREF="); printSwissProtProteinUrl(stdout, description); printf(">%s</A>",description); freez(&description); printf("</LI>" ); } } } else { /* display mrna */ printf("<LI><B>mRna:</B> %s \n", pg->name); linkToOtherBrowserExtra(database, pg->gChrom, pg->gStart, pg->gEnd, "mrna=pack"); printf("%s:%d-%d \n", pg->gChrom, pg->gStart, pg->gEnd); printf("</A></LI>"); } if (!sameString(pg->mgc,"noMgc")) { printf("<LI><B>%s Gene:</B> %s \n", mgcDbName(), pg->mgc); linkToOtherBrowserExtra(database, pg->gChrom, pg->mStart, pg->mEnd, "mgcGenes=pack"); printf("%s:%d-%d \n", pg->gChrom, pg->mStart, pg->mEnd); printf("</A></LI>"); } printf("</ul>"); /* display pfam domains */ printf("<p>"); pdb = hPdbFromGdb(database); safef(pfamDesc, 128, "%s.pfamDesc", pdb); if (hTableExists(database, "knownToPfam") && hTableExists(database, pfamDesc)) { sqlSafef(query, sizeof(query), "select description from knownToPfam kp, %s p where pfamAC = value and kp.name = '%s'", pfamDesc, pg->kgName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *description = row[0]; if (description == NULL) description = cloneString("n/a"); printf("<B>Pfam Domain:</B> %s <p>", description); } sqlFreeResult(&sr); } if (hTableExists(database, "all_mrna")) { char parent[255]; struct psl *pslList = NULL; char *dotPtr ; safef(parent, sizeof(parent), "%s",pg->name); /* strip off version and unique suffix when looking for parent gene*/ dotPtr = rStringIn(".",parent) ; if (dotPtr != NULL) *dotPtr = '\0'; pslList = loadPslRangeT("all_mrna", parent, pg->gChrom, pg->gStart, pg->gEnd); #ifdef NOT_USED char callClustal[512] = "YES"; char inPath[512]; safef(inPath, sizeof(inPath), "../pseudogene/pseudoHumanExp.%s.%s.%d.aln", pg->name, pg->chrom, pg->chromStart); /* either display a link to jalview or call it */ if (callClustal != NULL && sameString(callClustal, "YES")) { displayJalView(inPath, "CLUSTAL", NULL); printf(" Display alignment of retrogene and parent mRNAs. "); } // else // { // hgcAnchorJalview(pg->name, faTn.forCgi); // printf("JalView alignment of parent gene to retroGene</a>\n"); // } #endif /* NOT_USED */ if (pslList != NULL) { printAlignments(pslList, pslList->tStart, "htcCdnaAli", "all_mrna", \ pg->name); htmlHorizontalLine(); safef(chainTable_chrom,sizeof(chainTable_chrom), "%s_chainSelf",\ pg->chrom); if (hTableExists(database, chainTable_chrom) ) { /* lookup chain */ sqlDyStringPrintf(dy, "select id, score, qStart, qEnd, qStrand, qSize from %s_%s where ", pg->chrom, chainTable); hAddBinToQuery(pg->chromStart, pg->chromEnd, dy); if (sameString(pg->gStrand,pg->strand)) sqlDyStringPrintf(dy, "tEnd > %d and tStart < %d and qName = '%s' and qEnd > %d and qStart < %d and qStrand = '+' ", pg->chromStart, pg->chromEnd, pg->gChrom, pg->gStart, pg->gEnd); else { sqlDyStringPrintf(dy,"tEnd > %d and tStart < %d and qName = '%s' and qEnd > %d " "and qStart < %d and qStrand = '-'", pg->chromStart, pg->chromEnd, pg->gChrom, hChromSize(database, pg->gChrom)-(pg->gEnd), hChromSize(database, pg->gChrom)-(pg->gStart)); } dyStringAppend(dy, " order by qStart"); sr = sqlGetResult(conn, dy->string); while ((row = sqlNextRow(sr)) != NULL) { int chainId, score; unsigned int qStart, qEnd, qSize; char qStrand; if (first == 0) { printf("<H4>Gene/PseudoGene Alignment (multiple records are a result of breaks in the human Self Chaining)</H4>\n"); printf("Shows removed introns, frameshifts and in frame stops.\n"); first = 1; } chainId = sqlUnsigned(row[0]); score = sqlUnsigned(row[1]); qStart = sqlUnsigned(row[2]); qEnd = sqlUnsigned(row[3]); qStrand =row[4][0]; qSize = sqlUnsigned(row[5]); if (qStrand == '-') { unsigned int tmp = qSize - qEnd; qEnd = qSize - qStart; qStart = tmp; } /* if (pg->chainId == 0) pg->chainId = chainId; */ puts("<ul><LI>\n"); hgcAnchorPseudoGene(pg->kgName, "knownGene", pg->chrom, "startcodon", pg->chromStart, pg->chromEnd, pg->gChrom, pg->kStart, pg->kEnd, chainId, database); printf("Annotated alignment</a> using self chain.\n"); printf("Score: %d \n", score); puts("</LI>\n"); printf("<ul>Raw alignment: "); hgcAnchorTranslatedChain(chainId, chainTable, pg->chrom, pg->gStart, pg->gEnd); printf("%s:%d-%d </A></ul> </ul>\n", pg->gChrom,qStart,qEnd); } sqlFreeResult(&sr); } } } printf("<p>RetroGene Score: %d \n",pg->score); printf("Alignment Score: %d <br>\n",pg->axtScore); if (pg->posConf != 0) printf("AdaBoost Confidence:</B> %4.3f \n",pg->posConf); } void doPseudoPsl(struct trackDb *tdb, char *acc) /* Click on an pseudogene based on mrna alignment. */ { char *tableName = tdb->table; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; char where[256]; struct pseudoGeneLink *pg; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); int winStart = cartInt(cart, "l"); int winEnd = cartInt(cart, "r"); struct psl *pslList = NULL; char *chrom = cartString(cart, "c"); char *alignTable = cgiUsualString("table", cgiString("g")); int rowOffset = 0; /* Get alignment info. */ if (sameString(alignTable,"pseudoGeneLink2")) alignTable = cloneString("pseudoMrna2"); else if (sameString(alignTable,"pseudoGeneLink3")) alignTable = cloneString("pseudoMrna3"); else if (startsWith("pseudoGeneLink",alignTable)) alignTable = cloneString("pseudoMrna"); if (startsWith("pseudoUcsc",alignTable)) { alignTable = cloneString("pseudoMrna"); tableName = cloneString("pseudoGeneLink3"); } if (hTableExists(database, alignTable) ) { pslList = loadPslRangeT(alignTable, acc, chrom, winStart, winEnd); } else errAbort("Table %s not found.\n",alignTable); slSort(&pslList, pslCmpScoreDesc); /* print header */ genericHeader(tdb, acc); /* Print non-sequence info. */ cartWebStart(cart, database, "%s", acc); sqlSafefFrag(where, sizeof(where), "name = '%s'", acc); sr = hRangeQuery(conn, tableName, chrom, start, end, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { pg = pseudoGeneLinkLoad(row+rowOffset); if (pg != NULL) { pseudoPrintPos(pslList, pg, alignTable, start, acc); } } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doSoftberryPred(struct trackDb *tdb, char *geneName) /* Handle click on Softberry gene track. */ { genericHeader(tdb, geneName); showHomologies(geneName, "softberryHom"); if (sameWord(database, "sc1"))showSAM_T02(geneName); geneShowCommon(geneName, tdb, "softberryPep"); printTrackHtml(tdb); } void doPseudoPred(struct trackDb *tdb, char *geneName) /* Handle click on Softberry gene track. */ { genericHeader(tdb, geneName); showPseudoHomologies(geneName, "borkPseudoHom"); geneShowCommon(geneName, tdb, "borkPseudoPep"); printTrackHtml(tdb); } void doEncodePseudoPred(struct trackDb *tdb, char *geneName) { char query[256], *headerItem, *name2 = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int start = cartInt(cart, "o"); headerItem = cloneString(geneName); genericHeader(tdb, headerItem); printCustomUrl(tdb, geneName, FALSE); if ((sameString(tdb->table, "encodePseudogeneConsensus")) || (sameString(tdb->table, "encodePseudogeneYale"))) { sqlSafef(query, sizeof(query), "select name2 from %s where name = '%s'", tdb->table, geneName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { name2 = cloneString(row[0]); } printOtherCustomUrl(tdb, name2, "url2", TRUE); } genericGenePredClick(conn, tdb, geneName, start, NULL, NULL); printTrackHtml(tdb); hFreeConn(&conn); } void showOrthology(char *geneName, char *table, struct sqlConnection *connMm) /* Show mouse Orthlogous info. */ { char query[256]; struct sqlResult *sr; char **row; boolean isFirst = TRUE, gotAny = FALSE; char *gi; struct softberryHom hom; if (sqlTableExists(connMm, table)) { sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, geneName); sr = sqlGetResult(connMm, query); while ((row = sqlNextRow(sr)) != NULL) { softberryHomStaticLoad(row, &hom); if ((gi = getGi(hom.giString)) == NULL) continue; if (isFirst) { htmlHorizontalLine(); printf("<H3>Protein Homologies:</H3>\n"); isFirst = FALSE; gotAny = TRUE; } printf("<A HREF=\""); char temp[256]; safef(temp, sizeof(temp), "%s[gi]", gi); printEntrezProteinUrl(stdout, query); printf("\" TARGET=_blank>%s</A> %s<BR>", hom.giString, hom.description); } } if (gotAny) htmlHorizontalLine(); sqlFreeResult(&sr); } void doMouseOrtho(struct trackDb *tdb, char *geneName) /* Handle click on MouseOrtho gene track. */ { struct sqlConnection *connMm = sqlConnect(mousedb); genericHeader(tdb, geneName); showOrthology(geneName, "softberryHom",connMm); tdb = hashFindVal(trackHash, "softberryGene"); geneShowMouse(geneName, tdb, "softberryPep", connMm); printTrackHtml(tdb); sqlDisconnect(&connMm); } void showSangerExtra(char *geneName, char *extraTable) /* Show info from sanger22extra table if it exists. */ { if (hTableExists(database, extraTable)) { struct sanger22extra se; char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", extraTable, geneName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { sanger22extraStaticLoad(row, &se); printf("<B>Name:</B> %s<BR>\n", se.name); if (!sameString(se.name, se.locus)) printf("<B>Locus:</B> %s<BR>\n", se.locus); printf("<B>Description:</B> %s<BR>\n", se.description); printf("<B>Gene type:</B> %s<BR>\n", se.geneType); if (se.cdsType[0] != 0 && !sameString(se.geneType, se.cdsType)) printf("<B>CDS type:</B> %s<BR>\n", se.cdsType); } sqlFreeResult(&sr); hFreeConn(&conn); } } void doSangerGene(struct trackDb *tdb, char *geneName, char *pepTable, char *mrnaTable, char *extraTable) /* Handle click on Sanger gene track. */ { genericHeader(tdb, geneName); showSangerExtra(geneName, extraTable); geneShowCommon(geneName, tdb, pepTable); printTrackHtml(tdb); } void doTrnaGenesGb(struct trackDb *tdb, char *trnaName) { struct tRNAs *trna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb,trnaName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, ArraySize(query), "select * from %s where name = '%s' and chromStart=%d and chromEnd=%d", tdb->table, trnaName, start, end); sr = sqlGetResult(conn, query); /* use TABLE to align image with other info side by side */ printf("<TABLE>"); while ((row = sqlNextRow(sr)) != NULL) { char imgFileName[512]; char encodedName[255]; char *chp1, *chp2; int i, len; printf("<TR>"); printf("<TD valign=top>"); trna = tRNAsLoad(row+rowOffset); printf("<B>tRNA name: </B>%s<BR>\n",trna->name); printf("<B>tRNA isotype: </B> %s<BR>\n",trna->aa); printf("<B>tRNA anticodon: </B> %s<BR>\n",trna->ac); printf("<B>tRNAscan-SE score: </B> %.2f bits<BR>\n",trna->trnaScore); printf("<B>Intron(s): </B> %s<BR>\n",trna->intron); printf("<B>Genomic size: </B> %d nt<BR>\n",trna->chromEnd-trna->chromStart); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, trna->chrom, trna->chromStart+1, trna->chromEnd); printf("%s:%d-%d</A><BR>\n", trna->chrom, trna->chromStart+1, trna->chromEnd); printf("<B>Strand:</B> %s<BR>\n", trna->strand); if (!sameString(trna->genomeUrl, "")) { printf("<BR><A HREF=\"%s\" TARGET=_blank>View summary of all genomic tRNA predictions</A><BR>\n" , trna->genomeUrl); printf("<BR><A HREF=\"%s\" TARGET=_blank>View complete details for this tRNA</A><BR>\n", trna->trnaUrl); } if (trna->next != NULL) printf("<hr>\n"); printf("</TD>"); printf("<TD>"); /* encode '?' in tRNA name into "%3F" */ len = strlen(trna->name); chp1 = trna->name; chp2 = encodedName; for (i=0; i<len; i++) { if (*chp1 == '?') { *chp2 = '%'; chp2++; *chp2 = '3'; chp2++; *chp2 = 'F'; } else { *chp2 = *chp1; } chp1++; chp2++; } *chp2 = '\0'; safef(imgFileName, sizeof imgFileName, "../htdocs/RNA-img/%s/%s-%s.gif", database,database,trna->name); if (fileExists(imgFileName)) { printf( "<img align=right src=\"../RNA-img/%s/%s-%s.gif\" alt='tRNA secondary structure for %s'>\n", database,database,encodedName,trna->name); } else { printf( "<img align=right src=\"../RNA-img/%s/%s-%s.gif\" alt='tRNA secondary structure is not available for %s'>\n", database,database,trna->name,trna->name); } printf("</TD>"); printf("</TR>"); } printf("</TABLE>"); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); tRNAsFree(&trna); } void doVegaGeneZfish(struct trackDb *tdb, char *name) /* Handle click on Vega gene track for zebrafish. */ { struct vegaInfoZfish *vif = NULL; char query[256]; struct sqlResult *sr; char **row; genericHeader(tdb, name); if (hTableExists(database, "vegaInfoZfish")) { struct sqlConnection *conn = hAllocConn(database); sqlSafef(query, sizeof(query), "select * from vegaInfoZfish where transcriptId = '%s'", name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { AllocVar(vif); vegaInfoZfishStaticLoad(row, vif); } sqlFreeResult(&sr); hFreeConn(&conn); } printCustomUrl(tdb, name, TRUE); if (vif != NULL) { /* change confidence to lower case and display with method for gene type */ tolowers(vif->confidence); printf("<B>VEGA Gene Type:</B> %s %s<BR>\n", vif->confidence, vif->method); printf("<B>VEGA Gene Name:</B> %s<BR>\n", vif->sangerName); if (differentString(vif->geneDesc, "NULL")) printf("<B>VEGA Gene Description:</B> %s<BR>\n", vif->geneDesc); printf("<B>VEGA Gene Id:</B> %s<BR>\n", vif->geneId); printf("<B>VEGA Transcript Id:</B> %s<BR>\n", name); printf("<B>ZFIN Id:</B> "); printf("<A HREF=\"http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s\" TARGET=_blank>%s</A><BR>\n", vif->zfinId, vif->zfinId); printf("<B>Official ZFIN Gene Symbol:</B> %s<BR>\n", vif->zfinSymbol); /* get information for the cloneId from */ printf("<B>Clone Id:</B> \n"); struct sqlConnection *conn2 = hAllocConn(database); sqlSafef(query, sizeof(query), "select cloneId from vegaToCloneId where transcriptId = '%s'", name); sr = sqlGetResult(conn2, query); if ((row = sqlNextRow(sr)) != NULL) printf("%s", row[0]); while ((row = sqlNextRow(sr)) != NULL) { printf(" ,%s ", row[0]); } printf("<BR>\n"); sqlFreeResult(&sr); hFreeConn(&conn2); } geneShowCommon(name, tdb, "vegaPep"); printTrackHtml(tdb); } void doVegaGene(struct trackDb *tdb, char *item, char *itemForUrl) /* Handle click on Vega gene track. */ { struct vegaInfo *vi = NULL; char versionString[256]; char dateReference[256]; char headerTitle[512]; /* see if hgFixed.trackVersion exists */ boolean trackVersionExists = hTableExists("hgFixed", "trackVersion"); /* assume nothing found */ versionString[0] = 0; dateReference[0] = 0; if (trackVersionExists) { char query[256]; struct sqlConnection *conn = hAllocConn(database); sqlSafef(query, sizeof(query), "select version,dateReference from hgFixed.trackVersion where db = '%s' AND name = 'vegaGene' order by updateTime DESC limit 1", database); struct sqlResult *sr = sqlGetResult(conn, query); char **row; /* in case of NULL result from the table */ versionString[0] = 0; while ((row = sqlNextRow(sr)) != NULL) { safef(versionString, sizeof(versionString), "Vega %s", row[0]); safef(dateReference, sizeof(dateReference), "%s", row[1]); } sqlFreeResult(&sr); hFreeConn(&conn); } if (itemForUrl == NULL) itemForUrl = item; if (versionString[0]) safef(headerTitle, sizeof(headerTitle), "%s - %s", item, versionString); else safef(headerTitle, sizeof(headerTitle), "%s", item); genericHeader(tdb, headerTitle); if (hTableExists(database, "vegaInfo")) { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select * from vegaInfo where transcriptId = '%s'", item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { AllocVar(vi); vegaInfoStaticLoad(row, vi); } sqlFreeResult(&sr); hFreeConn(&conn); } /* No archive for Vega */ char *archive = NULL; printEnsemblOrVegaCustomUrl(tdb, itemForUrl, item == itemForUrl, archive); if (vi != NULL) { printf("<B>VEGA Gene Type:</B> %s<BR>\n", vi->method); printf("<B>VEGA Gene Name:</B> %s<BR>\n", vi->otterId); if (differentString(vi->geneDesc, "NULL")) printf("<B>VEGA Gene Description:</B> %s<BR>\n", vi->geneDesc); printf("<B>VEGA Gene Id:</B> %s<BR>\n", vi->geneId); printf("<B>VEGA Transcript Id:</B> %s<BR>\n", item); } geneShowCommon(item, tdb, "vegaPep"); printTrackHtml(tdb); } void doBDGPGene(struct trackDb *tdb, char *geneName) /* Show Berkeley Drosophila Genome Project gene info. */ { struct bdgpGeneInfo *bgi = NULL; struct flyBaseSwissProt *fbsp = NULL; char *geneTable = tdb->table; char *truncName = cloneString(geneName); char *ptr = strchr(truncName, '-'); char infoTable[128]; char pepTable[128]; char query[512]; if (ptr != NULL) *ptr = 0; safef(infoTable, sizeof(infoTable), "%sInfo", geneTable); genericHeader(tdb, geneName); if (hTableExists(database, infoTable)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select * from %s where bdgpName = \"%s\";", infoTable, truncName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { bgi = bdgpGeneInfoLoad(row); if (hTableExists(database, "flyBaseSwissProt")) { sqlSafef(query, sizeof(query), "select * from flyBaseSwissProt where flyBaseId = \"%s\"", bgi->flyBaseId); sqlFreeResult(&sr); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) fbsp = flyBaseSwissProtLoad(row); } } sqlFreeResult(&sr); hFreeConn(&conn); } if (bgi != NULL) { if (!sameString(bgi->symbol, geneName)) { printf("<B>Gene symbol:</B> %s<BR>\n", bgi->symbol); } if (fbsp != NULL) { printf("<B>SwissProt:</B> <A HREF="); printSwissProtProteinUrl(stdout, fbsp->swissProtId); printf(" TARGET=_BLANK>%s</A> (%s) %s<BR>\n", fbsp->swissProtId, fbsp->spSymbol, fbsp->spGeneName); } printf("<B>FlyBase:</B> <A HREF="); printFlyBaseUrl(stdout, bgi->flyBaseId); printf(" TARGET=_BLANK>%s</A><BR>\n", bgi->flyBaseId); printf("<B>BDGP:</B> <A HREF="); printBDGPUrl(stdout, truncName); printf(" TARGET=_BLANK>%s</A><BR>\n", truncName); } printCustomUrl(tdb, geneName, FALSE); showGenePos(geneName, tdb); if (bgi != NULL) { if (bgi->go != NULL && bgi->go[0] != 0) { struct sqlConnection *goConn = sqlMayConnect("go"); char *goTerm = NULL; char *words[10]; char buf[512]; int wordCount = chopCommas(bgi->go, words); int i; puts("<B>Gene Ontology terms from BDGP:</B> <BR>"); for (i=0; i < wordCount && words[i][0] != 0; i++) { if (i > 0 && sameWord(words[i], words[i-1])) continue; goTerm = ""; if (goConn != NULL) { sqlSafef(query, sizeof(query), "select name from term where acc = 'GO:%s';", words[i]); goTerm = sqlQuickQuery(goConn, query, buf, sizeof(buf)); if (goTerm == NULL) goTerm = ""; } printf(" GO:%s: %s<BR>\n", words[i], goTerm); } sqlDisconnect(&goConn); } if (bgi->cytorange != NULL && bgi->cytorange[0] != 0) { printf("<B>Cytorange:</B> %s<BR>", bgi->cytorange); } } printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); safef(pepTable, sizeof(pepTable), "%sPep", geneTable); if (hGenBankHaveSeq(database, geneName, pepTable)) { puts("<LI>\n"); hgcAnchorSomewhere("htcTranslatedProtein", geneName, pepTable, seqName); printf("Predicted Protein</A> \n"); puts("</LI>\n"); } puts("<LI>\n"); hgcAnchorSomewhere("htcGeneMrna", geneName, tdb->track, seqName); printf("%s</A> may be different from the genomic sequence.\n", "Predicted mRNA"); puts("</LI>\n"); puts("<LI>\n"); hgcAnchorSomewhere("htcGeneInGenome", geneName, tdb->track, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); printf("</UL>\n"); printTrackHtml(tdb); } char *pepTableFromType(char *type) /* If type (should be from tdb->type) starts with "genePred xxxx", * return "xxxx" as the pepTable for this track. */ { char *dupe, *words[16]; int wordCount; char *pepTable = NULL; dupe = cloneString(type); wordCount = chopLine(dupe, words); if (wordCount > 1 && sameWord(words[0], "genePred") && words[1] != NULL) pepTable = cloneString(words[1]); freeMem(dupe); return pepTable; } struct bed *getBedAndPrintPos(struct trackDb *tdb, char *name, int maxN) /* Dig up the bed for this item just to print the position. */ { struct bed *bed = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; char query[256]; char table[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; int n = atoi(tdb->type + 4); int start = cgiInt("o"); if (n < 3) n = 3; if (n > maxN) n = maxN; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d " "and name = '%s'", table, seqName, start, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+hasBin, n); bedPrintPos(bed, n, tdb); } sqlFreeResult(&sr); hFreeConn(&conn); return bed; } void printFBLinkLine(char *label, char *id) /* If id is not NULL/empty, print a label and link to FlyBase. */ { if (isNotEmpty(id)) { printf("<B>%s:</B> <A HREF=", label); printFlyBaseUrl(stdout, id); printf(" TARGET=_BLANK>%s</A><BR>\n", id); } } void showFlyBase2004Xref(char *xrefTable, char *geneName) /* Show FlyBase gene info provided as of late 2004 * (D. mel. v4.0 / D. pseud. 1.0). Assumes xrefTable exists * and matches flyBase2004Xref.sql! */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct flyBase2004Xref *xref = NULL; struct flyBaseSwissProt *fbsp = NULL; char query[512]; sqlSafef(query, sizeof(query), "select * from %s where name = \"%s\";", xrefTable, geneName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { xref = flyBase2004XrefLoad(row); if (hTableExists(database, "flyBaseSwissProt") && isNotEmpty(xref->fbgn)) { sqlSafef(query, sizeof(query), "select * from flyBaseSwissProt where flyBaseId = \"%s\"", xref->fbgn); sqlFreeResult(&sr); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) fbsp = flyBaseSwissProtLoad(row); } } sqlFreeResult(&sr); hFreeConn(&conn); if (xref != NULL) { if (isNotEmpty(xref->symbol) && !sameString(xref->symbol, geneName)) { printf("<B>Gene symbol:</B> %s<BR>\n", xref->symbol); } if (isNotEmpty(xref->synonyms)) { int last = strlen(xref->synonyms) - 1; if (xref->synonyms[last] == ',') xref->synonyms[last] = 0; printf("<B>Synonyms:</B> "); htmlTextOut(xref->synonyms); printf("<BR>\n"); } if (fbsp != NULL) { printf("<B>SwissProt:</B> <A HREF="); printSwissProtProteinUrl(stdout, fbsp->swissProtId); printf(" TARGET=_BLANK>%s</A> (%s) %s<BR>\n", fbsp->swissProtId, fbsp->spSymbol, fbsp->spGeneName); } if (isNotEmpty(xref->type)) printf("<B>Type:</B> %s<BR>\n", xref->type); printFBLinkLine("FlyBase Gene", xref->fbgn); printFBLinkLine("FlyBase Protein", xref->fbpp); printFBLinkLine("FlyBase Annotation", xref->fban); } } void doFlyBaseGene(struct trackDb *tdb, char *geneName) /* Show FlyBase gene info. */ { char *xrefTable = trackDbSettingOrDefault(tdb, "xrefTable", "flyBase2004Xref"); genericHeader(tdb, geneName); /* Note: if we need to expand to a different xref table definition, do * some checking here. For now, assume it's flyBase2004Xref-compatible: */ if (hTableExists(database, xrefTable)) showFlyBase2004Xref(xrefTable, geneName); printCustomUrl(tdb, geneName, FALSE); if (startsWith("genePred", tdb->type)) { char *pepTable = pepTableFromType(tdb->type); showGenePos(geneName, tdb); printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); if (pepTable != NULL && hGenBankHaveSeq(database, geneName, pepTable)) { puts("<LI>\n"); hgcAnchorSomewhere("htcTranslatedProtein", geneName, pepTable, seqName); printf("Predicted Protein</A> \n"); puts("</LI>\n"); } else errAbort("Doh, no go for %s from %s<BR>\n", geneName, pepTable); puts("<LI>\n"); hgcAnchorSomewhere("htcGeneMrna", geneName, tdb->track, seqName); printf("%s</A> may be different from the genomic sequence.\n", "Predicted mRNA"); puts("</LI>\n"); puts("<LI>\n"); hgcAnchorSomewhere("htcGeneInGenome", geneName, tdb->track, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); printf("</UL>\n"); } else if (startsWith("bed", tdb->type)) { struct bed *bed = getBedAndPrintPos(tdb, geneName, 4); if (bed != NULL && bed->strand[0] != 0) printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedFree(&bed); } printTrackHtml(tdb); } void doBGIGene(struct trackDb *tdb, char *geneName) /* Show Beijing Genomics Institute gene annotation info. */ { struct bgiGeneInfo *bgi = NULL; char *geneTable = tdb->table; char infoTable[128]; char pepTable[128]; char query[512]; safef(infoTable, sizeof(infoTable), "%sInfo", geneTable); genericHeader(tdb, geneName); if (hTableExists(database, infoTable)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select * from %s where name = \"%s\";", infoTable, geneName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) bgi = bgiGeneInfoLoad(row); sqlFreeResult(&sr); hFreeConn(&conn); } printCustomUrl(tdb, geneName, FALSE); showGenePos(geneName, tdb); if (bgi != NULL) { printf("<B>Annotation source:</B> %s<BR>\n", bgi->source); if (bgi->go != NULL && bgi->go[0] != 0 && !sameString(bgi->go, "None")) { struct sqlConnection *goConn = sqlMayConnect("go"); char *goTerm = NULL; char *words[16]; char buf[512]; int wordCount = chopCommas(bgi->go, words); int i; puts("<B>Gene Ontology terms from BGI:</B> <BR>"); for (i=0; i < wordCount && words[i][0] != 0; i++) { if (i > 0 && sameWord(words[i], words[i-1])) continue; goTerm = ""; if (goConn != NULL) { sqlSafef(query, sizeof(query), "select name from term where acc = 'GO:%s';", words[i]); goTerm = sqlQuickQuery(goConn, query, buf, sizeof(buf)); if (goTerm == NULL) goTerm = ""; } printf(" GO:%s: %s<BR>\n", words[i], goTerm); } sqlDisconnect(&goConn); } if (bgi->ipr != NULL && bgi->ipr[0] != 0 && !sameString(bgi->ipr, "None")) { char *words[16]; int wordCount = chopByChar(bgi->ipr, ';', words, ArraySize(words)); int i; printf("<B>Interpro terms from BGI:</B> <BR>\n"); for (i=0; i < wordCount && words[i][0] != 0; i++) { printf(" %s<BR>\n", words[i]); } } if (hTableExists(database, "bgiGeneSnp") && hTableExists(database, "bgiSnp")) { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); struct sqlResult *sr; struct sqlResult *sr2; struct bgiSnp snp; struct bgiGeneSnp gs; char **row; int rowOffset = hOffsetPastBin(database, seqName, "bgiSnp"); boolean init = FALSE; sqlSafef(query, sizeof(query), "select * from bgiGeneSnp where geneName = '%s'", geneName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (! init) { printf("<B>BGI SNPs associated with gene %s:</B> <BR>\n", geneName); init = TRUE; } bgiGeneSnpStaticLoad(row, &gs); sqlSafef(query, sizeof(query), "select * from bgiSnp where name = '%s'", gs.snpName); sr2 = sqlGetResult(conn2, query); if ((row = sqlNextRow(sr2)) != NULL) { bgiSnpStaticLoad(row+rowOffset, &snp); printf(" <A HREF=%s&g=bgiSnp&i=%s&db=%s&c=%s&o=%d&t=%d>%s</A>: %s", hgcPathAndSettings(), gs.snpName, database, seqName, snp.chromStart, snp.chromEnd, gs.snpName, gs.geneAssoc); if (gs.effect[0] != 0) printf(", %s", gs.effect); if (gs.phase[0] != 0) printf(", phase %c", gs.phase[0]); if (gs.siftComment[0] != 0) printf(", SIFT comment: %s", gs.siftComment); puts("<BR>"); } sqlFreeResult(&sr2); } sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn2); } } printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); safef(pepTable, sizeof(pepTable), "%sPep", geneTable); if (hGenBankHaveSeq(database, geneName, pepTable)) { puts("<LI>\n"); hgcAnchorSomewhere("htcTranslatedProtein", geneName, pepTable, seqName); printf("Predicted Protein</A> \n"); puts("</LI>\n"); } puts("<LI>\n"); hgcAnchorSomewhere("htcGeneMrna", geneName, tdb->track, seqName); printf("%s</A> may be different from the genomic sequence.\n", "Predicted mRNA"); puts("</LI>\n"); puts("<LI>\n"); hgcAnchorSomewhere("htcGeneInGenome", geneName, tdb->track, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); printf("</UL>\n"); printTrackHtml(tdb); } void doBGISnp(struct trackDb *tdb, char *itemName) /* Put up info on a Beijing Genomics Institute SNP. */ { char *table = tdb->table; struct bgiSnp snp; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { bgiSnpStaticLoad(row+rowOffset, &snp); bedPrintPos((struct bed *)&snp, 3, tdb); printf("<B>SNP Type:</B> %s<BR>\n", (snp.snpType[0] == 'S') ? "Substitution" : (snp.snpType[0] == 'I') ? "Insertion" : "Deletion"); printf("<B>SNP Sequence:</B> %s<BR>\n", snp.snpSeq); printf("<B>SNP in Broiler?:</B> %s<BR>\n", snp.inBroiler); printf("<B>SNP in Layer?:</B> %s<BR>\n", snp.inLayer); printf("<B>SNP in Silkie?:</B> %s<BR>\n", snp.inSilkie); if (hTableExists(database, "bgiGeneSnp") && hTableExists(database, "bgiGene")) { struct genePred *bg; struct sqlConnection *conn2 = hAllocConn(database); struct sqlConnection *conn3 = hAllocConn(database); struct sqlResult *sr2, *sr3; struct bgiGeneSnp gs; sqlSafef(query, sizeof(query), "select * from bgiGeneSnp where snpName = '%s'", snp.name); sr2 = sqlGetResult(conn2, query); while ((row = sqlNextRow(sr2)) != NULL) { bgiGeneSnpStaticLoad(row, &gs); sqlSafef(query, sizeof(query), "select * from bgiGene where name = '%s'", gs.geneName); sr3 = sqlGetResult(conn3, query); while ((row = sqlNextRow(sr3)) != NULL) { bg = genePredLoad(row); printf("<B>Associated gene:</B> <A HREF=%s&g=bgiGene&i=%s&c=%s&db=%s&o=%d&t=%d&l=%d&r=%d>%s</A>: %s", hgcPathAndSettings(), gs.geneName, seqName, database, bg->txStart, bg->txEnd, bg->txStart, bg->txEnd, gs.geneName, gs.geneAssoc); if (gs.effect[0] != 0) printf(" %s", gs.effect); if (gs.phase[0] != 0) printf(" phase %c", gs.phase[0]); if (gs.siftComment[0] != 0) printf(", SIFT comment: %s", gs.siftComment); puts("<BR>"); } sqlFreeResult(&sr3); } hFreeConn(&conn3); sqlFreeResult(&sr2); hFreeConn(&conn2); } printf("<B>Quality Scores:</B> %d in reference, %d in read<BR>\n", snp.qualChr, snp.qualReads); printf("<B>Left Primer Sequence:</B> %s<BR>\n", snp.primerL); printf("<B>Right Primer Sequence:</B> %s<BR>\n", snp.primerR); if (snp.snpType[0] != 'S') { if (snp.questionM[0] == 'H') printf("<B>Indel Confidence</B>: High\n"); if (snp.questionM[0] == 'L') printf("<B>Indel Confidence</B>: Low\n"); } } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void parseChromPointPos(char *pos, char *retChrom, int *retPos) /* Parse out chrN:123 into chrN and 123. */ { char *s, *e; int len; e = strchr(pos, ':'); if (e == NULL) errAbort("No : in chromosome point position %s", pos); len = e - pos; memcpy(retChrom, pos, len); retChrom[len] = 0; s = e+1; *retPos = atoi(s); } void doGenomicDups(struct trackDb *tdb, char *dupName) /* Handle click on genomic dup track. */ { struct genomicDups dup; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char oChrom[64]; int oStart; cartWebStart(cart, database, "Genomic Duplications"); printf("<H2>Genomic Duplication Region</H2>\n"); if (cgiVarExists("o")) { int start = cartInt(cart, "o"); int rowOffset = hOffsetPastBin(database, seqName, tdb->table); parseChromPointPos(dupName, oChrom, &oStart); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d " "and otherChrom = '%s' and otherStart = %d", tdb->table, seqName, start, oChrom, oStart); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr))) { genomicDupsStaticLoad(row+rowOffset, &dup); printf("<B>Region Position:</B> <A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, dup.chrom, dup.chromStart, dup.chromEnd); printf("%s:%d-%d</A><BR>\n", dup.chrom, dup.chromStart, dup.chromEnd); printf("<B>Other Position:</B> <A HREF=\"%s&db=%s&position=%s%%3A%d-%d\" TARGET=_blank>", hgTracksName(), database, dup.otherChrom, dup.otherStart, dup.otherEnd); printf("%s:%d-%d</A><BR>\n", dup.otherChrom, dup.otherStart, dup.otherEnd); printf("<B>Relative orientation:</B> %s<BR>\n", dup.strand); printf("<B>Percent identity:</B> %3.1f%%<BR>\n", 0.1*dup.score); printf("<B>Size:</B> %d<BR>\n", dup.alignB); printf("<B>Bases matching:</B> %d<BR>\n", dup.matchB); printf("<B>Bases not matching:</B> %d<BR>\n", dup.mismatchB); htmlHorizontalLine(); } } else { puts("<P>Click directly on a repeat for specific information on that repeat</P>"); } printTrackHtml(tdb); hFreeConn(&conn); } void htcExtSeq(char *item) /* Print out DNA from some external but indexed .fa file. */ { struct dnaSeq *seq; cartHtmlStart(item); seq = hExtSeq(database, item); printf("<PRE><TT>"); faWriteNext(stdout, item, seq->dna, seq->size); printf("</TT></PRE>"); freeDnaSeq(&seq); } void doBlatMouse(struct trackDb *tdb, char *itemName) /* Handle click on blatMouse track. */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); struct psl *pslList = NULL, *psl; char *tiNum = strrchr(itemName, '|'); boolean hasBin; char table[HDB_MAX_TABLE_STRING]; /* Print heading info including link to NCBI. */ if (tiNum != NULL) ++tiNum; cartWebStart(cart, database, "%s", itemName); printf("<H1>Information on Mouse %s %s</H1>", (tiNum == NULL ? "Contig" : "Read"), itemName); /* Print links to NCBI and to sequence. */ if (tiNum != NULL) { printf("Link to "); printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/Traces/trace.cgi?val=%s\" TARGET=_blank>", tiNum); printf("NCBI Trace Repository for %s\n</A><BR>\n", itemName); } printf("Get "); printf("<A HREF=\"%s&g=htcExtSeq&c=%s&l=%d&r=%d&i=%s\">", hgcPathAndSettings(), seqName, winStart, winEnd, itemName); printf("Mouse DNA</A><BR>\n"); /* Print info about mate pair. */ if (tiNum != NULL && sqlTableExists(conn, "mouseTraceInfo")) { char buf[256]; char *templateId; boolean gotMate = FALSE; sqlSafef(query, sizeof query, "select templateId from mouseTraceInfo where ti = '%s'", itemName); templateId = sqlQuickQuery(conn, query, buf, sizeof(buf)); if (templateId != NULL) { sqlSafef(query, sizeof query, "select ti from mouseTraceInfo where templateId = '%s'", templateId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *ti = row[0]; if (!sameString(ti, itemName)) { printf("Get "); printf("<A HREF=\"%s&g=htcExtSeq&c=%s&l=%d&r=%d&i=%s\">", hgcPathAndSettings(), seqName, winStart, winEnd, ti); printf("DNA for read on other end of plasmid</A><BR>\n"); gotMate = TRUE; } } sqlFreeResult(&sr); } if (!gotMate) printf("No read from other end of plasmid in database.<BR>\n"); } /* Get alignment info and print. */ printf("<H2>Alignments</H2>\n"); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where qName = '%s'", table, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row+hasBin); slAddHead(&pslList, psl); } sqlFreeResult(&sr); slReverse(&pslList); printAlignments(pslList, start, "htcBlatXeno", tdb->table, itemName); printTrackHtml(tdb); } boolean parseRange(char *range, char **retSeq, int *retStart, int *retEnd) /* Parse seq:start-end into components. */ { char *s, *e; s = strchr(range, ':'); if (s == NULL) return FALSE; *s++ = 0; e = strchr(s, '-'); if (e == NULL) return FALSE; *e++ = 0; if (!isdigit(s[0]) || !isdigit(e[0])) return FALSE; *retSeq = range; *retStart = atoi(s); *retEnd = atoi(e); return TRUE; } void mustParseRange(char *range, char **retSeq, int *retStart, int *retEnd) /* Parse seq:start-end or die. */ { if (!parseRange(range, retSeq, retStart, retEnd)) errAbort("Malformed range %s", range); } struct psl *loadPslAt(char *track, char *qName, int qStart, int qEnd, char *tName, int tStart, int tEnd) /* Load a specific psl */ { struct dyString *dy = newDyString(1024); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct sqlResult *sr; char **row; struct psl *psl; if (!hFindSplitTable(database, tName, track, table, sizeof table, &hasBin)) errAbort("track %s not found", track); sqlDyStringPrintf(dy, "select * from %s ", table); sqlDyStringPrintf(dy, "where qStart = %d ", qStart); sqlDyStringPrintf(dy, "and qEnd = %d ", qEnd); sqlDyStringPrintf(dy, "and qName = '%s' ", qName); sqlDyStringPrintf(dy, "and tStart = %d ", tStart); sqlDyStringPrintf(dy, "and tEnd = %d ", tEnd); sqlDyStringPrintf(dy, "and tName = '%s'", tName); sr = sqlGetResult(conn, dy->string); row = sqlNextRow(sr); if (row == NULL) errAbort("Couldn't loadPslAt %s:%d-%d", tName, tStart, tEnd); psl = pslLoad(row + hasBin); sqlFreeResult(&sr); freeDyString(&dy); hFreeConn(&conn); return psl; } struct psl *loadPslFromRangePair(char *track, char *rangePair) /* Load a specific psl given 'qName:qStart-qEnd tName:tStart-tEnd' in rangePair. */ { char *qRange, *tRange; char *qName, *tName; int qStart, qEnd, tStart, tEnd; qRange = nextWord(&rangePair); tRange = nextWord(&rangePair); if (tRange == NULL) errAbort("Expecting two ranges in loadPslFromRangePair"); mustParseRange(qRange, &qName, &qStart, &qEnd); mustParseRange(tRange, &tName, &tStart, &tEnd); return loadPslAt(track, qName, qStart, qEnd, tName, tStart, tEnd); } void longXenoPsl1Given(struct trackDb *tdb, char *item, char *otherOrg, char *otherChromTable, char *otherDb, struct psl *psl, char *pslTableName ) /* Put up cross-species alignment when the second species * sequence is in a nib file, AND psl record is given. */ { char otherString[256]; char *thisOrg = hOrganism(database); cartWebStart(cart, database, "%s", tdb->longLabel); printf("<B>%s position:</B> <a target=\"_blank\" href=\"%s?db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n", otherOrg, hgTracksName(), otherDb, psl->qName, psl->qStart+1, psl->qEnd, psl->qName, psl->qStart+1, psl->qEnd); printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart); printf("<B>%s position:</B> %s:%d-%d<BR>\n", thisOrg, psl->tName, psl->tStart+1, psl->tEnd); printf("<B>%s size:</B> %d<BR>\n", thisOrg, psl->tEnd - psl->tStart); printf("<B>Identical Bases:</B> %d<BR>\n", psl->match + psl->repMatch); printf("<B>Number of Gapless Aligning Blocks:</B> %d<BR>\n", psl->blockCount ); printf("<B>Percent identity within gapless aligning blocks:</B> %3.1f%%<BR>\n", 0.1*(1000 - pslCalcMilliBad(psl, FALSE))); printf("<B>Strand:</B> %s<BR>\n",psl->strand); printf("<B>Browser window position:</B> %s:%d-%d<BR>\n", seqName, winStart+1, winEnd); printf("<B>Browser window size:</B> %d<BR>\n", winEnd - winStart); safef(otherString, sizeof otherString, "%d&pslTable=%s&otherOrg=%s&otherChromTable=%s&otherDb=%s", psl->tStart, pslTableName, otherOrg, otherChromTable, otherDb); if (pslTrimToTargetRange(psl, winStart, winEnd) != NULL) { hgcAnchorSomewhere("htcLongXenoPsl2", item, otherString, psl->tName); printf("<BR>View details of parts of alignment within browser window</A>.<BR>\n"); } } /* Multipurpose function to show alignments in details pages where applicable */ void longXenoPsl1(struct trackDb *tdb, char *item, char *otherOrg, char *otherChromTable, char *otherDb) /* Put up cross-species alignment when the second species * sequence is in a nib file. */ { struct psl *psl = NULL; char otherString[256]; char *thisOrg = hOrganism(database); cartWebStart(cart, database, "%s", tdb->longLabel); psl = loadPslFromRangePair(tdb->table, item); printf("<B>%s position:</B> <a target=\"_blank\" href=\"%s?db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n", otherOrg, hgTracksName(), otherDb, psl->qName, psl->qStart+1, psl->qEnd, psl->qName, psl->qStart+1, psl->qEnd); printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart); printf("<B>%s position:</B> %s:%d-%d<BR>\n", thisOrg, psl->tName, psl->tStart+1, psl->tEnd); printf("<B>%s size:</B> %d<BR>\n", thisOrg, psl->tEnd - psl->tStart); printf("<B>Identical Bases:</B> %d<BR>\n", psl->match + psl->repMatch); printf("<B>Number of Gapless Aligning Blocks:</B> %d<BR>\n", psl->blockCount ); printf("<B>Percent identity within gapless aligning blocks:</B> %3.1f%%<BR>\n", 0.1*(1000 - pslCalcMilliBad(psl, FALSE))); printf("<B>Strand:</B> %s<BR>\n",psl->strand); printf("<B>Browser window position:</B> %s:%d-%d<BR>\n", seqName, winStart+1, winEnd); printf("<B>Browser window size:</B> %d<BR>\n", winEnd - winStart); safef(otherString, sizeof otherString, "%d&pslTable=%s&otherOrg=%s&otherChromTable=%s&otherDb=%s", psl->tStart, tdb->table, otherOrg, otherChromTable, otherDb); /* joni */ if (pslTrimToTargetRange(psl, winStart, winEnd) != NULL) { hgcAnchorSomewhere("htcLongXenoPsl2", item, otherString, psl->tName); printf("<BR>View details of parts of alignment within browser window</A>.<BR>\n"); } if (containsStringNoCase(otherDb, "zoo")) printf("<P><A HREF='%s&db=%s'>Go to the browser view of the %s</A><BR>\n", hgTracksPathAndSettings(), otherDb, otherOrg); printTrackHtml(tdb); } /* Multipurpose function to show alignments in details pages where applicable Show the URL from trackDb as well. Only used for the Chimp tracks right now. */ void longXenoPsl1Chimp(struct trackDb *tdb, char *item, char *otherOrg, char *otherChromTable, char *otherDb) /* Put up cross-species alignment when the second species * sequence is in a nib file. */ { struct psl *psl = NULL; char otherString[256]; char *cgiItem = cgiEncode(item); char *thisOrg = hOrganism(database); cartWebStart(cart, database, "%s", tdb->longLabel); psl = loadPslFromRangePair(tdb->table, item); printf("<B>%s position:</B> %s:%d-%d<BR>\n", otherOrg, psl->qName, psl->qStart+1, psl->qEnd); printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart); printf("<B>%s position:</B> %s:%d-%d<BR>\n", thisOrg, psl->tName, psl->tStart+1, psl->tEnd); printf("<B>%s size:</B> %d<BR>\n", thisOrg, psl->tEnd - psl->tStart); printf("<B>Identical Bases:</B> %d<BR>\n", psl->match + psl->repMatch); printf("<B>Number of Gapless Aligning Blocks:</B> %d<BR>\n", psl->blockCount ); printf("<B>Percent identity within gapless aligning blocks:</B> %3.1f%%<BR>\n", 0.1*(1000 - pslCalcMilliBad(psl, FALSE))); printf("<B>Strand:</B> %s<BR>\n",psl->strand); printf("<B>Browser window position:</B> %s:%d-%d<BR>\n", seqName, winStart+1, winEnd); printf("<B>Browser window size:</B> %d<BR>\n", winEnd - winStart); safef(otherString, sizeof otherString, "%d&pslTable=%s&otherOrg=%s&otherChromTable=%s&otherDb=%s", psl->tStart, tdb->table, otherOrg, otherChromTable, otherDb); printCustomUrl(tdb, item, TRUE); printTrackHtml(tdb); freez(&cgiItem); } void longXenoPsl1zoo2(struct trackDb *tdb, char *item, char *otherOrg, char *otherChromTable) /* Put up cross-species alignment when the second species * sequence is in a nib file. */ { struct psl *psl = NULL; char otherString[256]; char anotherString[256]; char *thisOrg = hOrganism(database); cartWebStart(cart, database, "%s", tdb->longLabel); psl = loadPslFromRangePair(tdb->table, item); printf("<B>%s position:</B> %s:%d-%d<BR>\n", otherOrg, psl->qName, psl->qStart+1, psl->qEnd); printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart); printf("<B>%s position:</B> %s:%d-%d<BR>\n", thisOrg, psl->tName, psl->tStart+1, psl->tEnd); printf("<B>%s size:</B> %d<BR>\n", thisOrg, psl->tEnd - psl->tStart); printf("<B>Identical Bases:</B> %d<BR>\n", psl->match + psl->repMatch); printf("<B>Number of Gapless Aligning Blocks:</B> %d<BR>\n", psl->blockCount ); printf("<B>Strand:</B> %s<BR>\n",psl->strand); printf("<B>Percent identity within gapless aligning blocks:</B> %3.1f%%<BR>\n", 0.1*(1000 - pslCalcMilliBad(psl, FALSE))); printf("<B>Browser window position:</B> %s:%d-%d<BR>\n", seqName, winStart, winEnd); printf("<B>Browser window size:</B> %d<BR>\n", winEnd - winStart); safef(anotherString, sizeof anotherString, "%s",otherOrg); toUpperN(anotherString,1); printf("Link to <a href=\"http://hgwdev-tcbruen.gi.ucsc.edu/cgi-bin/hgTracks?db=zoo%s1&position=chr1:%d-%d\">%s database</a><BR>\n", anotherString, psl->qStart, psl->qEnd, otherOrg); safef(otherString, sizeof otherString, "%d&pslTable=%s&otherOrg=%s&otherChromTable=%s", psl->tStart, tdb->table, otherOrg, otherChromTable); if (pslTrimToTargetRange(psl, winStart, winEnd) != NULL) { hgcAnchorSomewhere("htcLongXenoPsl2", item, otherString, psl->tName); printf("<BR>View details of parts of alignment within browser window</A>.<BR>\n"); } printTrackHtml(tdb); } void doAlignmentOtherDb(struct trackDb *tdb, char *item) /* Put up cross-species alignment when the second species * is another db, indicated by the 3rd word of tdb->type. */ { char *otherOrg; char *otherDb; char *words[8]; char *typeLine = cloneString(tdb->type); int wordCount = chopLine(typeLine, words); if (wordCount < 3 || !(sameString(words[0], "psl") && sameString(words[1], "xeno"))) errAbort("doAlignmentOtherDb: trackDb type must be \"psl xeno XXX\" where XXX is the name of the other database."); otherDb = words[2]; otherOrg = hOrganism(otherDb); longXenoPsl1(tdb, item, otherOrg, "chromInfo", otherDb); } void doMultAlignZoo(struct trackDb *tdb, char *item, char *otherName ) /* Put up cross-species alignment when the second species * sequence is in a nib file. */ { char chromStr[64]; /* Check to see if name is one of zoo names */ if (!(strcmp(otherName,"human") && strcmp(otherName,"chimp") && strcmp(otherName,"baboon") && strcmp(otherName,"cow") && strcmp(otherName,"pig") && strcmp(otherName,"cat") && strcmp(otherName,"dog") && strcmp(otherName,"mouse") && strcmp(otherName,"rat") && strcmp(otherName,"chicken") && strcmp(otherName,"fugu") && strcmp(otherName,"tetra") && strcmp(otherName,"zebrafish"))) { safef( chromStr, sizeof chromStr, "%sChrom" , otherName ); longXenoPsl1zoo2(tdb, item, otherName, chromStr ); } } struct chain *getChainFromRange(char *chainTable, char *chrom, int chromStart, int chromEnd) /* get a list of chains for a range */ { char chainTable_chrom[256]; struct dyString *dy = newDyString(128); struct chain *chainList = NULL; struct sqlConnection *conn = hAllocConn(database); safef(chainTable_chrom, 256, "%s_%s",chrom, chainTable); if (hTableExists(database, chainTable_chrom) ) { /* lookup chain if not stored */ char **row; struct sqlResult *sr = NULL; sqlDyStringPrintf(dy, "select id, score, qStart, qEnd, qStrand, qSize from %s where ", chainTable_chrom); hAddBinToQuery(chromStart, chromEnd, dy); dyStringPrintf(dy, "tEnd > %d and tStart < %d ", chromStart,chromEnd); dyStringAppend(dy, " order by qStart"); sr = sqlGetResult(conn, dy->string); while ((row = sqlNextRow(sr)) != NULL) { int chainId = 0; unsigned int qStart, qEnd, qSize; struct chain *chain = NULL; char qStrand; chainId = sqlUnsigned(row[0]); qStart = sqlUnsigned(row[2]); qEnd = sqlUnsigned(row[3]); qStrand =row[4][0]; qSize = sqlUnsigned(row[5]); if (qStrand == '-') { unsigned int tmp = qSize - qEnd; qEnd = qSize - qStart; qStart = tmp; } chain = NULL; if (chainId != 0) { chain = chainLoadIdRange(database, chainTable, chrom, chromStart, chromEnd, chainId); if (chain != NULL) slAddHead(&chainList, chain); } } sqlFreeResult(&sr); } return chainList; } void htcPseudoGene(char *htcCommand, char *item) /* Interface for selecting & displaying alignments from axtInfo * for an item from a genePred table. */ { struct genePred *gp = NULL; struct axtInfo *aiList = NULL; struct axt *axtList = NULL; struct sqlResult *sr; char **row; char trackTemp[256]; char *track = cartString(cart, "o"); char *chrom = cartString(cart, "c"); char *name = cartOptionalString(cart, "i"); char *db2 = cartString(cart, "db2"); int tStart = cgiInt("l"); int tEnd = cgiInt("r"); char *qChrom = cgiOptionalString("qc"); int chainId = cgiInt("ci"); int qStart = cgiInt("qs"); int qEnd = cgiInt("qe"); char table[HDB_MAX_TABLE_STRING]; char query[512]; char nibFile[512]; char qNibFile[512]; char qNibDir[512]; char tNibDir[512]; char path[512]; boolean hasBin; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2; struct hash *qChromHash = hashNew(0); struct cnFill *fill; struct chain *chain; struct dnaSeq *tChrom = NULL; cartWebStart(cart, database, "Alignment of %s in %s to pseudogene in %s", name, hOrganism(db2), hOrganism(database)); conn2 = hAllocConn(db2); /* get nibFile for pseudoGene */ sqlSafef(query, sizeof query, "select fileName from chromInfo where chrom = '%s'", chrom); if (sqlQuickQuery(conn, query, nibFile, sizeof(nibFile)) == NULL) errAbort("Sequence %s isn't in chromInfo", chrom); /* get nibFile for Gene in other species */ sqlSafef(query, sizeof query, "select fileName from chromInfo where chrom = '%s'" ,qChrom); if (sqlQuickQuery(conn2, query, qNibFile, sizeof(qNibFile)) == NULL) errAbort("Sequence chr1 isn't in chromInfo"); /* get gp */ if (!hFindSplitTable(db2, qChrom, track, table, sizeof table, &hasBin)) errAbort("htcPseudoGene: table %s not found.\n",track); else if (sameString(track, "mrna")) { struct psl *psl = NULL ; sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s' and tStart = %d ", table, name, qChrom, qStart ); sr = sqlGetResult(conn2, query); if ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row+hasBin); if (psl != NULL) gp = genePredFromPsl(psl, psl->tStart, psl->tEnd, 10); } sqlFreeResult(&sr); } else if (table != NULL) { sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' ", table, name, qChrom ); sr = sqlGetResult(conn2, query); if ((row = sqlNextRow(sr)) != NULL) gp = genePredLoad(row + hasBin); sqlFreeResult(&sr); } if (gp == NULL) errAbort("htcPseudoGene: Could not locate gene prediction (db=%s, table=%s, name=%s, in range %s:%d-%d) %s", db2, table, name, qChrom, qStart+1, qEnd, query); /* extract nib directory from nibfile */ if (strrchr(nibFile,'/') != NULL) strncpy(tNibDir, nibFile, strlen(nibFile)-strlen(strrchr(nibFile,'/'))); else errAbort("Cannot find nib directory for %s\n",nibFile); tNibDir[strlen(nibFile)-strlen(strrchr(nibFile,'/'))] = '\0'; if (strrchr(qNibFile,'/') != NULL) strncpy(qNibDir, qNibFile, strlen(qNibFile)-strlen(strrchr(qNibFile,'/'))); else errAbort("Cannot find nib directory for %s\n",qNibFile); qNibDir[strlen(qNibFile)-strlen(strrchr(qNibFile,'/'))] = '\0'; safef(path, sizeof path, "%s/%s.nib", tNibDir, chrom); /* load chain */ if (sameString(database,db2)) { track = "selfChain"; if (!hTableExists(database, "chr1_selfChain")) track = "chainSelf"; } else { safef(trackTemp, sizeof trackTemp, "%sChain",hOrganism(db2)); trackTemp[0] = tolower(trackTemp[0]); track = trackTemp; } if (chainId > 0 ) { chain = chainDbLoad(conn, database, track, chrom, chainId); /* get list of axts for a chain */ AllocVar(fill); fill->qName = cloneString(qChrom); fill->tSize = tEnd-tStart; fill->tStart = tStart; fill->chainId = chainId; fill->qSize = gp->txEnd - gp->txStart; fill->qStart = max(qStart, gp->txStart); fill->children = NULL; fill->next = NULL; fill->qStrand = chain->qStrand; tChrom = nibLoadPartMasked(NIB_MASK_MIXED, nibFile, fill->tStart, fill->tSize); axtList = netFillToAxt(fill, tChrom, hChromSize(database, chrom), qChromHash, qNibDir, chain, TRUE); /* make sure list is in correct order */ if (axtList != NULL) if (axtList->next != NULL) if ((gp->strand[0] == '+' && axtList->tStart > axtList->next->tStart) || (gp->strand[0] == '-' && axtList->tStart < axtList->next->tStart) ) slReverse(&axtList); /* fill in gaps between axt blocks */ /* allows display of aligned coding regions */ axtFillGap(&axtList,qNibDir, gp->strand[0]); if (gp->strand[0] == '-') axtListReverse(&axtList, database); if (axtList != NULL) if (axtList->next != NULL) if ((axtList->next->tStart < axtList->tStart && gp->strand[0] == '+') || (axtList->next->tStart > axtList->tStart && (gp->strand[0] == '-'))) slReverse(&axtList); /* output fancy formatted alignment */ puts("<PRE><TT>"); axtOneGeneOut(database, axtList, LINESIZE, stdout , gp, qNibFile); puts("</TT></PRE>"); } axtInfoFreeList(&aiList); hFreeConn(&conn2); } void htcLongXenoPsl2(char *htcCommand, char *item) /* Display alignment - loading sequence from nib file. */ { char *pslTable = cgiString("pslTable"); char *otherOrg = cgiString("otherOrg"); char *otherDb = cgiString("otherDb"); struct psl *psl = loadPslFromRangePair(pslTable, item); char *qChrom; char *ptr; char name[128]; struct dnaSeq *qSeq = NULL; /* In hg10 tables, psl->qName can be org.chrom. Strip it down to just * the chrom: */ qChrom = psl->qName; if ((ptr = strchr(qChrom, '.')) != NULL) qChrom = ptr+1; /* Make sure that otherOrg's chrom size matches psl's qSize */ if (hChromSize(database, qChrom) != psl->qSize) errAbort("Alignment's query size for %s is %d, but the size of %s in database %s is %d. Incorrect database in trackDb.type?", qChrom, psl->qSize, qChrom, otherDb, hChromSize(otherDb, qChrom)); psl = pslTrimToTargetRange(psl, winStart, winEnd); qSeq = loadGenomePart(otherDb, qChrom, psl->qStart, psl->qEnd); snprintf(name, sizeof(name), "%s.%s", otherOrg, qChrom); char title[1024]; safef(title, sizeof title, "%s %dk", name, psl->qStart/1000); htmlFramesetStart(title); showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, 0, 0); } void doAlignCompGeno(struct trackDb *tdb, char *itemName, char *otherGenome) /* Handle click on blat or blastz track in a generic fashion */ /* otherGenome is the text to display for genome name on details page */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *chrom = cartString(cart, "c"); struct psl *pslList = NULL, *psl; boolean hasBin; char table[HDB_MAX_TABLE_STRING]; char *typeLine = cloneString(tdb->type); char *words[8]; int wordCount = chopLine(typeLine, words); if (wordCount == 3) { if (sameString(words[0], "psl") && sameString(words[1], "xeno")) { /* words[2] will contain other db */ doAlignmentOtherDb(tdb, itemName); freeMem(typeLine); return; } } freeMem(typeLine); cartWebStart(cart, database, "%s", itemName); printPosOnChrom(chrom,start,end,NULL,FALSE,NULL); printf("<H1>Information on %s Sequence %s</H1>", otherGenome, itemName); printf("Get "); printf("<A HREF=\"%s&g=htcExtSeq&c=%s&l=%d&r=%d&i=%s\">", hgcPathAndSettings(), seqName, winStart, winEnd, itemName); printf("%s DNA</A><BR>\n", otherGenome); /* Get alignment info and print. */ printf("<H2>Alignments</H2>\n"); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("doAlignCompGeno track %s not found", tdb->table); /* if this is a non-split table then query with tName */ if (startsWith(tdb->table, table)) sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s'", table, itemName,seqName); else sqlSafef(query, sizeof(query), "select * from %s where qName = '%s'", table, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row+hasBin); slAddHead(&pslList, psl); } sqlFreeResult(&sr); slReverse(&pslList); printAlignments(pslList, start, "htcBlatXeno", tdb->table, itemName); printTrackHtml(tdb); } void doTSS(struct trackDb *tdb, char *itemName) /* Handle click on DBTSS track. */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; int start = cartInt(cart, "o"); struct psl *pslList = NULL, *psl = NULL; boolean hasBin = TRUE; char *table = "refFullAli"; /* Table with the pertinent PSL data */ cartWebStart(cart, database, "%s", itemName); printf("<H1>Information on DBTSS Sequence %s</H1>", itemName); printf("Get "); printf("<A HREF=\"%s&g=htcExtSeq&c=%s&l=%d&r=%d&i=%s\">", hgcPathAndSettings(), seqName, winStart, winEnd, itemName); printf("Sequence</A><BR>\n"); /* Get alignment info and print. */ printf("<H2>Alignments</H2>\n"); sqlSafef(query, sizeof query, "select * from %s where qName = '%s'", table, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row + hasBin); slAddHead(&pslList, psl); } sqlFreeResult(&sr); slReverse(&pslList); printAlignments(pslList, start, "htcCdnaAli", tdb->table, itemName); printTrackHtml(tdb); } void doEst3(char *itemName) /* Handle click on EST 3' end track. */ { struct est3 el; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; cartWebStart(cart, database, "EST 3' Ends"); printf("<H2>EST 3' Ends</H2>\n"); rowOffset = hOffsetPastBin(database, seqName, "est3"); sqlSafef(query, sizeof query, "select * from est3 where chrom = '%s' and chromStart = %d", seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { est3StaticLoad(row+rowOffset, &el); printf("<B>EST 3' End Count:</B> %d<BR>\n", el.estCount); bedPrintPos((struct bed *)&el, 3, NULL); printf("<B>strand:</B> %s<BR>\n", el.strand); htmlHorizontalLine(); } puts("<P>This track shows where clusters of EST 3' ends hit the " "genome. In many cases these represent the 3' ends of genes. " "This data was kindly provided by Lukas Wagner and Greg Schuler " "at NCBI. Additional filtering was applied by Jim Kent.</P>"); sqlFreeResult(&sr); hFreeConn(&conn); } void doEncodeRna(struct trackDb *tdb, char *itemName) /* Handle click on encodeRna track. */ { struct encodeRna rna; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; struct slName *nameList, *sl; genericHeader(tdb, itemName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d and name = '%s'", tdb->table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { encodeRnaStaticLoad(row + rowOffset, &rna); printf("<B>name:</B> %s<BR>\n", rna.name); bedPrintPos((struct bed *)&rna, 3, tdb); printf("<B>strand:</B> %s<BR>\n", rna.strand); printf("<B>type:</B> %s<BR>\n", rna.type); printf("<B>score:</B> %2.1f<BR><BR>\n", rna.fullScore); printf("<B>is pseudo-gene:</B> %s<BR>\n", (rna.isPsuedo ? "yes" : "no")); printf("<B>is Repeatmasked:</B> %s<BR>\n", (rna.isRmasked ? "yes" : "no")); printf("<B>is Transcribed:</B> %s<BR>\n", (rna.isTranscribed ? "yes" : "no")); printf("<B>is an evoFold prediction:</B> %s<BR>\n", (rna.isPrediction ? "yes" : "no")); printf("<B>program predicted with:</B> %s<BR>\n", rna.source); printf("<BR><B>This region is transcribed in: </B>"); nameList = slNameListFromString(rna.transcribedIn,','); if(nameList==NULL||sameString(nameList->name,".")) printf("<BR> Not transcribed\n"); else for (sl=nameList;sl!=NULL;sl=sl->next) printf("<BR> %s\n",sl->name); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doRnaGene(struct trackDb *tdb, char *itemName) /* Handle click on RNA Genes track. */ { struct rnaGene rna; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; genericHeader(tdb, itemName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d and name = '%s'", tdb->table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { rnaGeneStaticLoad(row + rowOffset, &rna); printf("<B>name:</B> %s<BR>\n", rna.name); printf("<B>type:</B> %s<BR>\n", rna.type); printf("<B>score:</B> %2.1f<BR>\n", rna.fullScore); printf("<B>is pseudo-gene:</B> %s<BR>\n", (rna.isPsuedo ? "yes" : "no")); printf("<B>program predicted with:</B> %s<BR>\n", rna.source); printf("<B>strand:</B> %s<BR>\n", rna.strand); bedPrintPos((struct bed *)&rna, 3, tdb); htmlHorizontalLine(); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doStsMarker(struct trackDb *tdb, char *marker) /* Respond to click on an STS marker. */ { char *table = tdb->table; char query[256]; char title[256]; struct sqlConnection *conn = hAllocConn(database); boolean stsInfo2Exists = sqlTableExists(conn, "stsInfo2"); boolean stsInfoExists = sqlTableExists(conn, "stsInfo"); boolean stsMapExists = sqlTableExists(conn, "stsMap"); struct sqlConnection *conn1 = hAllocConn(database); struct sqlResult *sr = NULL, *sr1 = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct stsMap stsRow; struct stsInfo *infoRow = NULL; struct stsInfo2 *info2Row = NULL; char stsid[20]; int i; struct psl *pslList = NULL, *psl; int pslStart; char *sqlMarker = marker; boolean hasBin; /* Make sure to escpae single quotes for DB parseability */ if (strchr(marker, '\'')) sqlMarker = replaceChars(marker, "'", "''"); /* Print out non-sequence info */ safef(title, sizeof title, "STS Marker %s", marker); cartWebStart(cart, database, "%s", title); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", table, sqlMarker, seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); hasBin = hOffsetPastBin(database, seqName, table); if (row != NULL) { if (stsMapExists) stsMapStaticLoad(row+hasBin, &stsRow); else /* Load and convert from original bed format */ { struct stsMarker oldStsRow; stsMarkerStaticLoad(row+hasBin, &oldStsRow); stsMapFromStsMarker(&oldStsRow, &stsRow); } if (stsInfo2Exists) { /* Find the instance of the object in the stsInfo2 table */ sqlFreeResult(&sr); sqlSafef(query, sizeof query, "SELECT * FROM stsInfo2 WHERE identNo = '%d'", stsRow.identNo); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { int i; char **cl; cl = (char **)needMem(52*sizeof(char *)); for (i = 0; i < 52; ++i) cl[i] = cloneString(row[i]); info2Row = stsInfo2Load(row); infoRow = stsInfoLoad(cl); freeMem(cl); } } else if (stsInfoExists) { /* Find the instance of the object in the stsInfo table */ sqlFreeResult(&sr); sqlSafef(query, sizeof query, "SELECT * FROM stsInfo WHERE identNo = '%d'", stsRow.identNo); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) infoRow = stsInfoLoad(row); } if (((stsInfo2Exists) || (stsInfoExists)) && (row != NULL)) { printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printBand(seqName, start, end, TRUE); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out marker name and links to UniSTS, Genebank, GDB */ if (infoRow->nameCount > 0) { printf("<TABLE>\n"); printf("<TR><TH>Other names:</TH><TD>%s",infoRow->otherNames[0]); for (i = 1; i < infoRow->nameCount; i++) printf(", %s",infoRow->otherNames[i]); printf("</TD></TR>\n</TABLE>\n"); htmlHorizontalLine(); } printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>UCSC STS id:</TH><TD>%d</TD></TR>\n", stsRow.identNo); printf("<TR><TH ALIGN=left>UniSTS id:</TH><TD><A HREF="); printUnistsUrl(stdout, infoRow->dbSTSid); printf(" TARGET=_BLANK>%d</A></TD></TR>\n", infoRow->dbSTSid); if (infoRow->otherDbstsCount > 0) { printf("<TR><TH ALIGN=left>Related UniSTS ids:</TH>"); for (i = 0; i < infoRow->otherDbstsCount; i++) { printf("<TD><A HREF="); printUnistsUrl(stdout, infoRow->otherDbSTS[i]); printf(" TARGET=_BLANK>%d</A></TD>", infoRow->otherDbSTS[i]); } printf("</TR>\n"); } if (infoRow->gbCount > 0) { printf("<TR><TH ALIGN=left>Genbank:</TH>"); for (i = 0; i < infoRow->gbCount; i++) { printf("<TD><A HREF=\""); printEntrezNucleotideUrl(stdout, infoRow->genbank[i]); printf("\" TARGET=_BLANK>%s</A></TD>", infoRow->genbank[i]); } printf("</TR>\n"); } if (infoRow->gdbCount > 0) { printf("<TR><TH ALIGN=left>GDB:</TH>"); for (i = 0; i < infoRow->gdbCount; i++) { printf("<TD>"); printf("%s</TD>", infoRow->gdb[i]); } printf("</TR>\n"); } printf("<TR><TH ALIGN=left>Organism:</TH><TD>%s</TD></TR>\n",infoRow->organism); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out primer information */ if (!sameString(infoRow->leftPrimer,"")) { printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Left Primer:</TH><TD>%s</TD></TR>\n",infoRow->leftPrimer); printf("<TR><TH ALIGN=left>Right Primer:</TH><TD>%s</TD></TR>\n",infoRow->rightPrimer); printf("<TR><TH ALIGN=left>Distance:</TH><TD>%s bps</TD></TR>\n",infoRow->distance); printf("</TABLE>\n"); htmlHorizontalLine(); } /* Print out information from STS maps for this marker */ if ((!sameString(infoRow->genethonName,"")) || (!sameString(infoRow->marshfieldName,"")) || (stsInfo2Exists && info2Row != NULL && (!sameString(info2Row->decodeName,"")))) { printf("<H3>Genetic Map Positions</H3>\n"); printf("<TABLE>\n"); printf("<TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); if (!sameString(infoRow->genethonName,"")) printf("<TH ALIGN=left>Genethon:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->genethonName, infoRow->genethonChr, infoRow->genethonPos); if (!sameString(infoRow->marshfieldName,"")) printf("<TH ALIGN=left>Marshfield:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->marshfieldName, infoRow->marshfieldChr, infoRow->marshfieldPos); if ((stsInfo2Exists) && (!sameString(info2Row->decodeName,""))) printf("<TH ALIGN=left>deCODE:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", info2Row->decodeName, info2Row->decodeChr, info2Row->decodePos); printf("</TABLE><P>\n"); } if (!sameString(infoRow->wiyacName,"")) { printf("<H3>Whitehead YAC Map Position</H3>\n"); printf("<TABLE>\n"); printf("<TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TH ALIGN=left>WI YAC:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->wiyacName, infoRow->wiyacChr, infoRow->wiyacPos); printf("</TABLE><P>\n"); } if ((!sameString(infoRow->wirhName,"")) || (!sameString(infoRow->gm99gb4Name,"")) || (!sameString(infoRow->gm99g3Name,"")) || (!sameString(infoRow->tngName,""))) { printf("<H3>RH Map Positions</H3>\n"); printf("<TABLE>\n"); if ((!sameString(infoRow->wirhName,"")) || (!sameString(infoRow->gm99gb4Name,"")) || (!sameString(infoRow->gm99g3Name,""))) printf("<TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position (LOD)</TH></TR>\n"); else printf("<TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); if (!sameString(infoRow->gm99gb4Name,"")) printf("<TH ALIGN=left>GM99 Gb4:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f (%.2f)</TD></TR>\n", infoRow->gm99gb4Name, infoRow->gm99gb4Chr, infoRow->gm99gb4Pos, infoRow->gm99gb4LOD); if (!sameString(infoRow->gm99g3Name,"")) printf("<TH ALIGN=left>GM99 G3:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f (%.2f)</TD></TR>\n", infoRow->gm99g3Name, infoRow->gm99g3Chr, infoRow->gm99g3Pos, infoRow->gm99g3LOD); if (!sameString(infoRow->wirhName,"")) printf("<TH ALIGN=left>WI RH:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f (%.2f)</TD></TR>\n", infoRow->wirhName, infoRow->wirhChr, infoRow->wirhPos, infoRow->wirhLOD); if (!sameString(infoRow->tngName,"")) printf("<TH ALIGN=left>Stanford TNG:</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->tngName, infoRow->tngChr, infoRow->tngPos); printf("</TABLE><P>\n"); } /* Print out alignment information - full sequence */ webNewSection("Genomic Alignments:"); sqlSafef(query, sizeof query, "SELECT * FROM all_sts_seq WHERE qName = '%d'", infoRow->identNo); sr1 = sqlGetResult(conn1, query); hasBin = hOffsetPastBin(database, seqName, "all_sts_seq"); i = 0; pslStart = 0; while ((row = sqlNextRow(sr1)) != NULL) { psl = pslLoad(row+hasBin); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Full sequence:</H3>\n"); safef(stsid, sizeof stsid, "%d", infoRow->identNo); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_seq", stsid); sqlFreeResult(&sr1); htmlHorizontalLine(); } slFreeList(&pslList); /* Print out alignment information - primers */ safef(stsid, sizeof stsid, "dbSTS_%d", infoRow->dbSTSid); sqlSafef(query, sizeof query, "SELECT * FROM all_sts_primer WHERE qName = '%s'", stsid); hasBin = hOffsetPastBin(database, seqName, "all_sts_primer"); sr1 = sqlGetResult(conn1, query); i = 0; pslStart = 0; while ((row = sqlNextRow(sr1)) != NULL) { psl = pslLoad(row+hasBin); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Primers:</H3>\n"); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_primer", stsid); sqlFreeResult(&sr1); } slFreeList(&pslList); stsInfoFree(&infoRow); } else { printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Position:</TH><TD>%d</TD></TR>\n", (stsRow.chromStart+stsRow.chromEnd)>>1); printf("<TR><TH ALIGN=left>UCSC STS id:</TH><TD>%d</TD></TR>\n", stsRow.identNo); if (!sameString(stsRow.ctgAcc, "-")) printf("<TR><TH ALIGN=left>Clone placed on:</TH><TD>%s</TD></TR>\n", stsRow.ctgAcc); if (!sameString(stsRow.otherAcc, "-")) printf("<TR><TH ALIGN=left>Other clones hit:</TH><TD>%s</TD></TR>\n", stsRow.otherAcc); if (!sameString(stsRow.genethonChrom, "0")) printf("<TR><TH ALIGN=left>Genethon:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.genethonChrom, stsRow.genethonPos); if (!sameString(stsRow.marshfieldChrom, "0")) printf("<TR><TH ALIGN=left>Marshfield:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.marshfieldChrom, stsRow.marshfieldPos); if (!sameString(stsRow.gm99Gb4Chrom, "0")) printf("<TR><TH ALIGN=left>GeneMap99 GB4:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.gm99Gb4Chrom, stsRow.gm99Gb4Pos); if (!sameString(stsRow.shgcG3Chrom, "0")) printf("<TR><TH ALIGN=left>GeneMap99 G3:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.shgcG3Chrom, stsRow.shgcG3Pos); if (!sameString(stsRow.wiYacChrom, "0")) printf("<TR><TH ALIGN=left>Whitehead YAC:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.wiYacChrom, stsRow.wiYacPos); if (!sameString(stsRow.wiRhChrom, "0")) printf("<TR><TH ALIGN=left>Whitehead RH:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.wiRhChrom, stsRow.wiRhPos); if (!sameString(stsRow.shgcTngChrom, "0")) printf("<TR><TH ALIGN=left>Stanford TNG:</TH><TD>chr%s</TD><TD>%.2f</TD></TR>\n", stsRow.shgcTngChrom, stsRow.shgcTngPos); if (!sameString(stsRow.fishChrom, "0")) printf("<TR><TH ALIGN=left>FISH:</TH><TD>%s.%s - %s.%s</TD></TR>\n", stsRow.fishChrom, stsRow.beginBand, stsRow.fishChrom, stsRow.endBand); printf("</TABLE>\n"); htmlHorizontalLine(); if (stsRow.score == 1000) printf("<H3>This is the only location found for %s</H3>\n",marker); else { sqlFreeResult(&sr); printf("<H4>Other locations found for %s in the genome:</H4>\n", marker); printf("<TABLE>\n"); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND (chrom != '%s' OR chromStart != %d OR chromEnd != %d)", table, marker, seqName, start, end); sr = sqlGetResult(conn,query); hasBin = hOffsetPastBin(database, seqName, table); while ((row = sqlNextRow(sr)) != NULL) { if (stsMapExists) stsMapStaticLoad(row+hasBin, &stsRow); else /* Load and convert from original bed format */ { struct stsMarker oldStsRow; stsMarkerStaticLoad(row+hasBin, &oldStsRow); stsMapFromStsMarker(&oldStsRow, &stsRow); } printf("<TR><TD>%s:</TD><TD>%d</TD></TR>\n", stsRow.chrom, (stsRow.chromStart+stsRow.chromEnd)>>1); } printf("</TABLE>\n"); } htmlHorizontalLine(); } } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn1); } void doStsMapMouse(struct trackDb *tdb, char *marker) /* Respond to click on an STS marker. */ { char *table = tdb->table; char title[256]; char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn1 = hAllocConn(database); struct sqlResult *sr = NULL, *sr1 = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *hgsid = cartSessionId(cart); struct stsMapMouse stsRow; struct stsInfoMouse *infoRow; char stsid[20]; int i; struct psl *pslList = NULL, *psl; int pslStart; /* Print out non-sequence info */ safef(title, sizeof title, "STS Marker %s", marker); cartWebStart(cart, database, "%s", title); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", table, marker, seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { stsMapMouseStaticLoad(row, &stsRow); /* Find the instance of the object in the stsInfo table */ sqlFreeResult(&sr); sqlSafef(query, sizeof query, "SELECT * FROM stsInfoMouse WHERE identNo = '%d'", stsRow.identNo); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { infoRow = stsInfoMouseLoad(row); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printf("</TABLE>\n"); htmlHorizontalLine(); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>MGI Marker ID:</TH><TD><B>MGI:</B>"); printf("<A HREF = \"http://www.informatics.jax.org/marker/MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIMarkerID, infoRow->MGIMarkerID); printf("<TR><TH ALIGN=left>MGI Probe ID:</TH><TD><B>MGI:</B>"); printf("<A HREF = \"http://www.informatics.jax.org/marker/MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIPrimerID, infoRow->MGIPrimerID); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out primer information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Left Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer1); printf("<TR><TH ALIGN=left>Right Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer2); printf("<TR><TH ALIGN=left>Distance:</TH><TD>%s bps</TD></TR>\n",infoRow->distance); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out information from genetic maps for this marker */ printf("<H3>Genetic Map Position</H3>\n"); printf("<TABLE>\n"); printf("<TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->stsMarkerName, infoRow->Chr, infoRow->geneticPos); printf("</TABLE><P>\n"); /* Print out alignment information - full sequence */ webNewSection("Genomic Alignments:"); safef(stsid, sizeof stsid, "%d", infoRow->MGIPrimerID); sqlSafef(query, sizeof query, "SELECT * FROM all_sts_primer" " WHERE qName = '%s' AND tStart = '%d' AND tEnd = '%d'",stsid, start, end); sr1 = sqlGetResult(conn1, query); i = 0; pslStart = 0; while ((row = sqlNextRow(sr1)) != NULL) { psl = pslLoad(row); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Primers:</H3>\n"); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_primer", stsid); sqlFreeResult(&sr1); } slFreeList(&pslList); stsInfoMouseFree(&infoRow); } htmlHorizontalLine(); if (stsRow.score == 1000) printf("<H3>This is the only location found for %s</H3>\n",marker); else { sqlFreeResult(&sr); printf("<H4>Other locations found for %s in the genome:</H4>\n", marker); printf("<TABLE>\n"); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND (chrom != '%s' OR chromStart != %d OR chromEnd != %d)", table, marker, seqName, start, end); sr = sqlGetResult(conn,query); while ((row = sqlNextRow(sr)) != NULL) { stsMapMouseStaticLoad(row, &stsRow); printf("<TR><TD>%s:</TD><TD><A HREF = \"../cgi-bin/hgc?hgsid=%s&o=%u&t=%d&g=stsMapMouse&i=%s&c=%s\" target=_blank>%d</A></TD></TR>\n", stsRow.chrom, hgsid, stsRow.chromStart,stsRow.chromEnd, stsRow.name, stsRow.chrom,(stsRow.chromStart+stsRow.chromEnd)>>1); } printf("</TABLE>\n"); } } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn1); } void doStsMapMouseNew(struct trackDb *tdb, char *marker) /* Respond to click on an STS marker. */ { char *table = tdb->table; char title[256]; char query[256]; char query1[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn1 = hAllocConn(database); struct sqlResult *sr = NULL, *sr1 = NULL, *sr2 = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *hgsid = cartSessionId(cart); struct stsMapMouseNew stsRow; struct stsInfoMouseNew *infoRow; char stsid[20]; char stsPrimer[40]; char stsClone[45]; int i; struct psl *pslList = NULL, *psl; int pslStart; char sChar='%'; /* Print out non-sequence info */ safef(title, sizeof title, "STS Marker %s\n", marker); /* safef(title, sizeof title, "STS Marker <A HREF=\"http://www.informatics.jax.org/searches/marker_report.cgi?string\%%3AmousemarkerID=%s\" TARGET=_BLANK>%s</A>\n", marker, marker); */ cartWebStart(cart, database, "%s", title); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", table, marker, seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { stsMapMouseNewStaticLoad(row, &stsRow); /* Find the instance of the object in the stsInfo table */ sqlFreeResult(&sr); sqlSafef(query, sizeof query, "SELECT * FROM stsInfoMouseNew WHERE identNo = '%d'", stsRow.identNo); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { infoRow = stsInfoMouseNewLoad(row); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printf("</TABLE>\n"); htmlHorizontalLine(); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>UCSC STS Marker ID:</TH><TD>%d</TD></TR>\n", infoRow->identNo); if (infoRow->UiStsId != 0) printf("<TR><TH ALIGN=left>UniSts Marker ID:</TH><TD>" "<A HREF=\"https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%d\" " "TARGET=_BLANK>%d</A></TD></TR>\n", infoRow->UiStsId, infoRow->UiStsId); if (infoRow->MGIId != 0) printf("<TR><TH ALIGN=left>MGI Marker ID:</TH><TD><B>" "<A HREF=\"http://www.informatics.jax.org/searches/marker_report.cgi?" "accID=MGI%c3A%d\" TARGET=_BLANK>%d</A></TD></TR>\n", sChar,infoRow->MGIId,infoRow->MGIId ); if (strcmp(infoRow->MGIName, "")) printf("<TR><TH ALIGN=left>MGI Marker Name:</TH><TD>%s</TD></TR>\n", infoRow->MGIName); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out primer information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Left Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer1); printf("<TR><TH ALIGN=left>Right Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer2); printf("<TR><TH ALIGN=left>Distance:</TH><TD>%s bps</TD></TR>\n",infoRow->distance); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out information from genetic maps for this marker */ if(strcmp(infoRow->wigName, "") || strcmp(infoRow->mgiName, "") || strcmp(infoRow->rhName, "")) printf("<H3>Map Position</H3>\n<TABLE>\n"); if(strcmp(infoRow->wigName, "")) { printf("<TR><TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TR><TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->wigName, infoRow->wigChr, infoRow->wigGeneticPos); } if (strcmp(infoRow->mgiName, "")) { printf("<TR><TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TR><TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->mgiName, infoRow->mgiChr, infoRow->mgiGeneticPos); } if (strcmp(infoRow->rhName, "")) { printf("<TR><TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH><TH ALIGN=left WIDTH=150>Score</TH?</TR>\n"); printf("<TR><TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->rhName, infoRow->rhChr, infoRow->rhGeneticPos, infoRow->RHLOD); } printf("</TABLE><P>\n"); /* Print out alignment information - full sequence */ webNewSection("Genomic Alignments:"); safef(stsid, sizeof stsid, "%d", infoRow->identNo); safef(stsPrimer, sizeof stsPrimer, "%d_%s", infoRow->identNo, infoRow->name); safef(stsClone, sizeof stsClone, "%d_%s_clone", infoRow->identNo, infoRow->name); /* find sts in primer alignment info */ sqlSafef(query, sizeof query, "SELECT * FROM all_sts_primer WHERE qName = '%s' AND tStart = '%d' " "AND tEnd = '%d'",stsPrimer, start, end); sr1 = sqlGetResult(conn1, query); i = 0; pslStart = 0; while ((row = sqlNextRow(sr1)) != NULL ) { psl = pslLoad(row); fflush(stdout); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Primers:</H3>\n"); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_primer", stsPrimer); sqlFreeResult(&sr1); } slFreeList(&pslList); stsInfoMouseNewFree(&infoRow); /* Find sts in clone sequece alignment info */ sqlSafef(query1, sizeof query1, "SELECT * FROM all_sts_primer WHERE qName = '%s' AND tStart = '%d' AND tEnd = '%d'",stsClone, start, end); sr2 = sqlGetResult(conn1, query1); i = 0; pslStart = 0; while ((row = sqlNextRow(sr2)) != NULL ) { psl = pslLoad(row); fflush(stdout); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Clone:</H3>\n"); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_primer", stsClone); sqlFreeResult(&sr1); } slFreeList(&pslList); stsInfoMouseNewFree(&infoRow); } htmlHorizontalLine(); if (stsRow.score == 1000) printf("<H3>This is the only location found for %s</H3>\n",marker); else { sqlFreeResult(&sr); printf("<H4>Other locations found for %s in the genome:</H4>\n", marker); printf("<TABLE>\n"); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND (chrom != '%s' OR chromStart != %d OR chromEnd != %d)", table, marker, seqName, start, end); sr = sqlGetResult(conn,query); while ((row = sqlNextRow(sr)) != NULL) { stsMapMouseNewStaticLoad(row, &stsRow); printf("<TR><TD>%s:</TD><TD><A HREF = \"../cgi-bin/hgc?hgsid=%s&o=%u&t=%d&" "g=stsMapMouseNew&i=%s&c=%s\" target=_blank>%d</A></TD></TR>\n", stsRow.chrom, hgsid, stsRow.chromStart,stsRow.chromEnd, stsRow.name, stsRow.chrom,(stsRow.chromStart+stsRow.chromEnd)>>1); } printf("</TABLE>\n"); } } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn1); } void doStsMapRat(struct trackDb *tdb, char *marker) /* Respond to click on an STS marker. */ { char *table = tdb->table; char title[256]; char query[256]; char query1[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn1 = hAllocConn(database); struct sqlResult *sr = NULL, *sr1 = NULL, *sr2 = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *hgsid = cartSessionId(cart); struct stsMapRat stsRow; struct stsInfoRat *infoRow; char stsid[20]; char stsPrimer[40]; char stsClone[45]; int i; struct psl *pslList = NULL, *psl; int pslStart; boolean hasBin = FALSE; /* Print out non-sequence info */ safef(title, sizeof title, "STS Marker %s", marker); cartWebStart(cart, database, "%s", title); /* Find the instance of the object in the bed table */ sqlSafefFrag(query, sizeof(query), "name = '%s'", marker); sr = hRangeQuery(conn, table, seqName, start, end, query, &hasBin); row = sqlNextRow(sr); if (row != NULL) { stsMapRatStaticLoad(row+hasBin, &stsRow); /* Find the instance of the object in the stsInfo table */ sqlFreeResult(&sr); sqlSafef(query, sizeof query, "SELECT * FROM stsInfoRat WHERE identNo = '%d'", stsRow.identNo); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { infoRow = stsInfoRatLoad(row); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printf("</TABLE>\n"); htmlHorizontalLine(); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>UCSC STS Marker ID:</TH><TD>%d</TD></TR>\n", infoRow->identNo); if (infoRow->UiStsId != 0) printf("<TR><TH ALIGN=left>UniSts Marker ID:</TH><TD>" "<A HREF=\"https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%d\" " "TARGET=_BLANK>%d</A></TD></TR>\n", infoRow->UiStsId, infoRow->UiStsId); if (infoRow->RGDId != 0) printf("<TR><TH ALIGN=left>RGD Marker ID:</TH><TD><B>" "<A HREF=\"http://rgd.mcw.edu/tools/query/query.cgi?id=%d\" " "TARGET=_BLANK>%d</A></TD></TR>\n", infoRow->RGDId,infoRow->RGDId ); if (strcmp(infoRow->RGDName, "")) printf("<TR><TH ALIGN=left>RGD Marker Name:</TH><TD>%s</TD></TR>\n", infoRow->RGDName); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out primer information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Left Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer1); printf("<TR><TH ALIGN=left>Right Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer2); printf("<TR><TH ALIGN=left>Distance:</TH><TD>%s bps</TD></TR>\n",infoRow->distance); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out information from genetic maps for this marker */ if(strcmp(infoRow->fhhName, "") || strcmp(infoRow->shrspName, "") || strcmp(infoRow->rhName, "")) printf("<H3>Map Position</H3>\n<TABLE>\n"); if(strcmp(infoRow->fhhName, "")) { printf("<TR><TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TR><TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->fhhName, infoRow->fhhChr, infoRow->fhhGeneticPos); } if(strcmp(infoRow->shrspName, "")) { printf("<TR><TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TR><TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->shrspName, infoRow->shrspChr, infoRow->shrspGeneticPos); } if(strcmp(infoRow->rhName, "")) { printf("<TR><TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH><TH ALIGN=left WIDTH=150>Score</TH?</TR>\n"); printf("<TR><TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->rhName, infoRow->rhChr, infoRow->rhGeneticPos, infoRow->RHLOD); } printf("</TABLE><P>\n"); /* Print out alignment information - full sequence */ webNewSection("Genomic Alignments:"); safef(stsid, sizeof stsid, "%d", infoRow->identNo); safef(stsPrimer, sizeof stsPrimer, "%d_%s", infoRow->identNo, infoRow->name); safef(stsClone, sizeof stsClone, "%d_%s_clone", infoRow->identNo, infoRow->name); /* find sts in primer alignment info */ sqlSafefFrag(query, sizeof(query), "qName = '%s'", stsPrimer); sr1 = hRangeQuery(conn1, "all_sts_primer", seqName, start, end, query, &hasBin); i = 0; pslStart = 0; while ((row = sqlNextRow(sr1)) != NULL ) { psl = pslLoad(row+hasBin); fflush(stdout); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Primers:</H3>\n"); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_primer", stsPrimer); sqlFreeResult(&sr1); } slFreeList(&pslList); stsInfoRatFree(&infoRow); /* Find sts in clone sequece alignment info */ sqlSafefFrag(query1, sizeof(query1), "qName = '%s'", stsClone); sr2 = hRangeQuery(conn1, "all_sts_primer", seqName, start, end, query1, &hasBin); i = 0; pslStart = 0; while ((row = sqlNextRow(sr2)) != NULL ) { psl = pslLoad(row+hasBin); fflush(stdout); if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000)) pslStart = psl->tStart; slAddHead(&pslList, psl); i++; } slReverse(&pslList); if (i > 0) { printf("<H3>Clone:</H3>\n"); printAlignments(pslList, pslStart, "htcCdnaAli", "all_sts_primer", stsClone); sqlFreeResult(&sr1); } slFreeList(&pslList); stsInfoRatFree(&infoRow); } htmlHorizontalLine(); if (stsRow.score == 1000) printf("<H3>This is the only location found for %s</H3>\n",marker); else { sqlFreeResult(&sr); printf("<H4>Other locations found for %s in the genome:</H4>\n", marker); printf("<TABLE>\n"); sqlSafefFrag(query, sizeof(query), "name = '%s'", marker); sr = hRangeQuery(conn, table, seqName, start, end, query, &hasBin); while ((row = sqlNextRow(sr)) != NULL) { stsMapRatStaticLoad(row+hasBin, &stsRow); printf("<TR><TD>%s:</TD><TD><A HREF = \"../cgi-bin/hgc?hgsid=%s&o=%u&t=%d&g=stsMapRat&i=%s&c=%s\" target=_blank>%d</A></TD></TR>\n", stsRow.chrom, hgsid, stsRow.chromStart,stsRow.chromEnd, stsRow.name, stsRow.chrom,(stsRow.chromStart+stsRow.chromEnd)>>1); } printf("</TABLE>\n"); } } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn1); } void doFishClones(struct trackDb *tdb, char *clone) /* Handle click on the FISH clones track */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct fishClones *fc; int i; /* Print out non-sequence info */ cartWebStart(cart, database, "%s", clone); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM fishClones WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", clone, seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { fc = fishClonesLoad(row); /* Print out general sequence positional information */ printf("<H2><A HREF="); printCloneDbUrl(stdout, clone); printf(" TARGET=_BLANK>%s</A></H2>\n", clone); htmlHorizontalLine(); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printBand(seqName, start, end, TRUE); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out information about the clone */ printf("<H4>Placement of %s on draft sequence was determined using the location of %s</H4>\n", clone, fc->placeType); printf("<TABLE>\n"); if (fc->accCount > 0) { printf("<TR><TH>Genbank Accession:</TH>"); for (i = 0; i < fc->accCount; i++) { printf("<TD><A HREF=\""); printEntrezNucleotideUrl(stdout, fc->accNames[i]); printf("\" TARGET=_BLANK>%s</A></TD>", fc->accNames[i]); } printf("</TR>\n"); } if (fc->stsCount > 0) { printf("<TR><TH ALIGN=left>STS Markers within clone:</TH>"); for (i = 0; i < fc->stsCount; i++) { printf("<TD>%s</TD>", fc->stsNames[i]); } printf("</TR>\n"); } if (fc->beCount > 0) { printf("<TR><TH ALIGN=left>BAC end sequence:</TH>"); for (i = 0; i < fc->beCount; i++) { printf("<TD><A HREF=\""); printEntrezNucleotideUrl(stdout, fc->beNames[i]); printf("\" TARGET=_BLANK>%s</A></TD>", fc->beNames[i]); } printf("</TR>\n"); } printf("</TABLE>\n"); /* Print out FISH placement information */ webNewSection("FISH Placements"); /*printf("<H3>Placements of %s by FISH</H3>\n", clone);*/ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left WIDTH=100>Lab</TH><TH>Band Position</TH></TR>\n"); for (i = 0; i < fc->placeCount; i++) { if (sameString(fc->bandStarts[i],fc->bandEnds[i])) { printf("<TR><TD WIDTH=100 ALIGN=left>%s</TD><TD ALIGN=center>%s</TD></TR>", fc->labs[i], fc->bandStarts[i]); } else { printf("<TR><TD WIDTH=100 ALIGN=left>%s</TD><TD ALIGN=center>%s - %s</TD></TR>", fc->labs[i], fc->bandStarts[i], fc->bandEnds[i]); } } } printf("</TABLE>\n"); webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doRecombRate(struct trackDb *tdb) /* Handle click on the Recombination Rate track */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct recombRate *rr; /* Print out non-sequence info */ cartWebStart(cart, database, "Recombination Rates"); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM recombRate WHERE " "chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { rr = recombRateLoad(row); /* Print out general sequence positional information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printBand(seqName, start, end, TRUE); printf("<TR><TH ALIGN=left>deCODE Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->decodeAvg); printf("<TR><TH ALIGN=left>deCODE Female Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->decodeFemale); printf("<TR><TH ALIGN=left>deCODE Male Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->decodeMale); printf("<TR><TH ALIGN=left>Marshfield Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->marshfieldAvg); printf("<TR><TH ALIGN=left>Marshfield Female Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->marshfieldFemale); printf("<TR><TH ALIGN=left>Marshfield Male Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->marshfieldMale); printf("<TR><TH ALIGN=left>Genethon Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->genethonAvg); printf("<TR><TH ALIGN=left>Genethon Female Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->genethonFemale); printf("<TR><TH ALIGN=left>Genethon Male Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->genethonMale); printf("</TABLE>\n"); freeMem(rr); } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doRecombRateRat(struct trackDb *tdb) /* Handle click on the rat Recombination Rate track */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct recombRateRat *rr; /* Print out non-sequence info */ cartWebStart(cart, database, "Recombination Rates"); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM recombRateRat WHERE " "chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { rr = recombRateRatLoad(row); /* Print out general sequence positional information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printBand(seqName, start, end, TRUE); printf("<TR><TH ALIGN=left>SHRSPxBN Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->shrspAvg); printf("<TR><TH ALIGN=left>FHHxACI Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->fhhAvg); printf("</TABLE>\n"); freeMem(rr); } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doRecombRateMouse(struct trackDb *tdb) /* Handle click on the mouse Recombination Rate track */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct recombRateMouse *rr; /* Print out non-sequence info */ cartWebStart(cart, database, "Recombination Rates"); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM recombRateMouse WHERE " "chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { rr = recombRateMouseLoad(row); /* Print out general sequence positional information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printBand(seqName, start, end, TRUE); printf("<TR><TH ALIGN=left>WI Genetic Map Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->wiAvg); printf("<TR><TH ALIGN=left>MGD Genetic Map Sex-Averaged Rate:</TH><TD>%3.1f cM/Mb</TD></TR>\n", rr->mgdAvg); printf("</TABLE>\n"); freeMem(rr); } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doGenMapDb(struct trackDb *tdb, char *clone) /* Handle click on the GenMapDb clones track */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct genMapDb *upc; int size; /* Print out non-sequence info */ cartWebStart(cart, database, "GenMapDB BAC Clones"); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM genMapDb WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", clone, seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { upc = genMapDbLoad(row); /* Print out general sequence positional information */ printf("<H2><A HREF="); printGenMapDbUrl(stdout, clone); printf(" TARGET=_BLANK>%s</A></H2>\n", clone); htmlHorizontalLine(); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); size = end - start + 1; printf("<TR><TH ALIGN=left>Size:</TH><TD>%d</TD></TR>\n",size); printBand(seqName, start, end, TRUE); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out information about the clone */ printf("<H4>Placement of %s on draft sequence was determined using BAC end sequences and/or an STS marker</H4>\n",clone); printf("<TABLE>\n"); if (upc->accT7) { printf("<TR><TH ALIGN=left>T7 end sequence:</TH>"); printf("<TD><A HREF=\""); printEntrezNucleotideUrl(stdout, upc->accT7); printf("\" TARGET=_BLANK>%s</A></TD>", upc->accT7); printf("<TD>%s:</TD><TD ALIGN=right>%d</TD><TD ALIGN=LEFT> - %d</TD>", seqName, upc->startT7, upc->endT7); printf("</TR>\n"); } if (upc->accSP6) { printf("<TR><TH ALIGN=left>SP6 end sequence:</TH>"); printf("<TD><A HREF=\""); printEntrezNucleotideUrl(stdout, upc->accSP6); printf("\" TARGET=_BLANK>%s</A></TD>", upc->accSP6); printf("<TD>%s:</TD><TD ALIGN=right>%d</TD><TD ALIGN=LEFT> - %d</TD>", seqName, upc->startSP6, upc->endSP6); printf("</TR>\n"); } if (upc->stsMarker) { printf("<TR><TH ALIGN=left>STS Marker:</TH>"); printf("<TD><A HREF=\""); printEntrezUniSTSUrl(stdout, upc->stsMarker); printf("\" TARGET=_BLANK>%s</A></TD>", upc->stsMarker); printf("<TD>%s:</TD><TD ALIGN=right>%d</TD><TD ALIGN=LEFT> - %d</TD>", seqName, upc->stsStart, upc->stsEnd); printf("</TR>\n"); } printf("</TABLE>\n"); } webNewSection("Notes:"); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doMouseOrthoDetail(struct trackDb *tdb, char *itemName) /* Handle click on mouse synteny track. */ { struct mouseSyn el; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; cartWebStart(cart, database, "Mouse Synteny"); printf("<H2>Mouse Synteny</H2>\n"); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d", tdb->table, seqName, start); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { htmlHorizontalLine(); mouseSynStaticLoad(row+rowOffset, &el); printf("<B>mouse chromosome:</B> %s<BR>\n", el.name+6); printf("<B>human chromosome:</B> %s<BR>\n", skipChr(el.chrom)); printf("<B>human starting base:</B> %d<BR>\n", el.chromStart); printf("<B>human ending base:</B> %d<BR>\n", el.chromEnd); printf("<B>size:</B> %d<BR>\n", el.chromEnd - el.chromStart); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doMouseSyn(struct trackDb *tdb, char *itemName) /* Handle click on mouse synteny track. */ { struct mouseSyn el; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; cartWebStart(cart, database, "Mouse Synteny"); printf("<H2>Mouse Synteny</H2>\n"); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d", tdb->table, seqName, start); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { htmlHorizontalLine(); mouseSynStaticLoad(row+rowOffset, &el); printf("<B>mouse chromosome:</B> %s<BR>\n", el.name+6); printf("<B>human chromosome:</B> %s<BR>\n", skipChr(el.chrom)); printf("<B>human starting base:</B> %d<BR>\n", el.chromStart); printf("<B>human ending base:</B> %d<BR>\n", el.chromEnd); printf("<B>size:</B> %d<BR>\n", el.chromEnd - el.chromStart); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doMouseSynWhd(struct trackDb *tdb, char *itemName) /* Handle click on Whitehead mouse synteny track. */ { struct mouseSynWhd el; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; cartWebStart(cart, database, "Mouse Synteny (Whitehead)"); printf("<H2>Mouse Synteny (Whitehead)</H2>\n"); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d", tdb->table, seqName, start); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { htmlHorizontalLine(); mouseSynWhdStaticLoad(row+rowOffset, &el); printf("<B>mouse chromosome:</B> %s<BR>\n", el.name); printf("<B>mouse starting base:</B> %d<BR>\n", el.mouseStart+1); printf("<B>mouse ending base:</B> %d<BR>\n", el.mouseEnd); printf("<B>human chromosome:</B> %s<BR>\n", skipChr(el.chrom)); printf("<B>human starting base:</B> %d<BR>\n", el.chromStart+1); printf("<B>human ending base:</B> %d<BR>\n", el.chromEnd); printf("<B>strand:</B> %s<BR>\n", el.strand); printf("<B>segment label:</B> %s<BR>\n", el.segLabel); printf("<B>size:</B> %d (mouse), %d (human)<BR>\n", (el.mouseEnd - el.mouseStart), (el.chromEnd - el.chromStart)); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doEnsPhusionBlast(struct trackDb *tdb, char *itemName) /* Handle click on Ensembl Phusion Blast synteny track. */ { struct ensPhusionBlast el; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char *org = hOrganism(database); char *tbl = cgiUsualString("table", cgiString("g")); char *elname, *ptr, *xenoDb, *xenoOrg, *xenoChrom; char query[256]; int rowOffset; cartWebStart(cart, database, "%s", tdb->longLabel); printf("<H2>%s</H2>\n", tdb->longLabel); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d", tdb->table, seqName, start); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { htmlHorizontalLine(); ensPhusionBlastStaticLoad(row+rowOffset, &el); elname = cloneString(el.name); if ((ptr = strchr(elname, '.')) != NULL) { *ptr = 0; xenoChrom = ptr+1; xenoDb = elname; xenoOrg = hOrganism(xenoDb); } else { xenoChrom = elname; xenoDb = NULL; xenoOrg = "Other Organism"; } printf("<B>%s chromosome:</B> %s<BR>\n", xenoOrg, xenoChrom); printf("<B>%s starting base:</B> %d<BR>\n", xenoOrg, el.xenoStart+1); printf("<B>%s ending base:</B> %d<BR>\n", xenoOrg, el.xenoEnd); printf("<B>%s chromosome:</B> %s<BR>\n", org, skipChr(el.chrom)); printf("<B>%s starting base:</B> %d<BR>\n", org, el.chromStart+1); printf("<B>%s ending base:</B> %d<BR>\n", org, el.chromEnd); printf("<B>score:</B> %d<BR>\n", el.score); printf("<B>strand:</B> %s<BR>\n", el.strand); printf("<B>size:</B> %d (%s), %d (%s)<BR>\n", (el.xenoEnd - el.xenoStart), xenoOrg, (el.chromEnd - el.chromStart), org); if (xenoDb != NULL) { printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\" TARGET=_BLANK>%s Genome Browser</A> at %s:%d-%d <BR>\n", hgTracksName(), xenoDb, xenoChrom, el.xenoStart, el.xenoEnd, xenoOrg, xenoChrom, el.xenoStart, el.xenoEnd); } printf("<A HREF=\"%s&o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&strand=%s&table=%s\">" "View DNA for this feature</A><BR>\n", hgcPathAndSettings(), el.chromStart, cgiEncode(el.name), el.chrom, el.chromStart, el.chromEnd, el.strand, tbl); freez(&elname); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void printDbSnpRsUrl(char *rsId, char *labelFormat, ...) /* Print a link to dbSNP's report page for an rs[0-9]+ ID. */ { char dbSnpUrl[2048]; safef (dbSnpUrl, sizeof(dbSnpUrl), dbSnpFormat, rsId); printf ("<a href=\"%s\" target=\"_blank\">", dbSnpUrl); va_list args; va_start(args, labelFormat); vprintf(labelFormat, args); va_end(args); printf("</a>"); } char *validateOrGetRsId(char *name, struct sqlConnection *conn) /* If necessary, get the rsId from the affy120K or affy10K table, given the affyId. rsId is more common, affy120K is next, affy10K least. * returns "valid" if name is already a valid rsId, new rsId if it is found in the affy tables, or 0 if no valid rsId is found */ { char *rsId = cloneString(name); struct affy120KDetails *a120K = NULL; struct affy10KDetails *a10K = NULL; char query[512]; if (strncmp(rsId,"rs",2)) /* is not a valid rsId, so it must be an affyId */ { sqlSafef(query, sizeof(query), /* more likely to be affy120K, so check first */ "select * from affy120KDetails where affyId = '%s'", name); a120K = affy120KDetailsLoadByQuery(conn, query); if (a120K != NULL) /* found affy120K record */ rsId = cloneString(a120K->rsId); affy120KDetailsFree(&a120K); if (strncmp(rsId,"rs",2)) /* not a valid affy120K snp, might be affy10K */ { sqlSafef(query, sizeof(query), "select * from affy10KDetails where affyId = '%s'", name); a10K = affy10KDetailsLoadByQuery(conn, query); if (a10K != NULL) /* found affy10K record */ rsId = cloneString(a10K->rsId); affy10KDetailsFree(&a10K); if (strncmp(rsId,"rs",2)) /* not valid affy10K snp */ return 0; } /* not all affy snps have valid rsIds, so return if it is invalid */ if (strncmp(rsId,"rs",2) || strlen(rsId)<4 || sameString(rsId,"rs0")) /* not a valid rsId */ return 0; } else rsId = cloneString("valid"); return rsId; } char *doDbSnpRs(char *name) /* print additional SNP details * returns "valid" if name is already a valid rsId, new rsId if it is found in the affy tables, or 0 if no valid rsId is found */ { struct sqlConnection *hgFixed = sqlConnect("hgFixed"); char *rsId = validateOrGetRsId(name, hgFixed); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[512]; struct dbSnpRs *snp = NULL; char *dbOrg = cloneStringZ(database,2); toUpperN(dbOrg,1); /* capitalize first letter */ if (rsId) /* a valid rsId exists */ { if (sameString(rsId, "valid")) sqlSafef(query, sizeof(query), "select * " "from dbSnpRs%s " "where rsId = '%s'", dbOrg, name); else sqlSafef(query, sizeof(query), "select * " "from dbSnpRs%s " "where rsId = '%s'", dbOrg, rsId); snp = dbSnpRsLoadByQuery(hgFixed, query); if (snp != NULL) { printf("<BR>\n"); if(snp->avHetSE>0) { printf("<B><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html\" target=\"_blank\">"); printf("Average Heterozygosity</A>:</B> %f<BR>\n",snp->avHet); printf("<B><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html\" target=\"_blank\">"); printf("Standard Error of Avg. Het.</A>: </B> %f<BR>\n", snp->avHetSE); } else { printf("<B><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html\" target=\"_blank\">"); printf("Average Heterozygosity</A>:</B> Not Known<BR>\n"); printf("<B><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html\" target=\"_blank\">"); printf("Standard Error of Avg. Het.</A>: </B> Not Known<BR>\n"); } // printf("<B><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=snpFxnColor\" " // "target=\"_blank\">"); // printf("Functional Status</A>:</B> <span style='font-family:Courier;'>%s<BR></span>\n", // snp->func); printf("<B>Functional Status:</B> <span style='font-family:Courier;'>%s<BR></span>\n", snp->func); printf("<B><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=validation\" " "target=\"_blank\">"); printf("Validation Status</A>:</B> <span style='font-family:Courier;'>%s<BR></span>\n", snp->valid); // printf("<B>Validation Status:</B> <span style='font-family:Courier;'>%s<BR></span>\n", // snp->valid); printf("<B>Allele1: </B> <span style='font-family:Courier;'>%s<BR></span>\n", snp->allele1); printf("<B>Allele2: </B> <span style='font-family:Courier;'>%s<BR>\n", snp->allele2); printf("<B>Sequence in Assembly</B>: %s<BR>\n", snp->assembly); printf("<B>Alternate Sequence</B>: %s<BR></span>\n", snp->alternate); } dbSnpRsFree(&snp); } sqlDisconnect(&hgFixed); if (sameString(dbOrg,"Hg")) { sqlSafef(query, sizeof(query), "select source, type from snpMap where name = '%s'", name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("<B><A HREF=\"#source\">Variant Source</A></B>: %s<BR>\n",row[0]); printf("<B><A HREF=\"#type\">Variant Type</A></B>: %s\n",row[1]); } sqlFreeResult(&sr); hFreeConn(&conn); } return rsId; } void doSnpEntrezGeneLink(struct trackDb *tdb, char *name) /* print link to EntrezGene for this SNP */ { struct sqlConnection *conn = hAllocConn(database); char *table = tdb->table; if (hTableExists(database, "knownGene") && sqlTableExists(conn, refLinkTable) && hTableExists(database, "mrnaRefseq") && hTableExists(database, table)) { struct sqlResult *sr; char **row; char query[512]; sqlSafef(query, sizeof(query), "select distinct " " rl.locusLinkID, " " rl.name " "from knownGene kg, " " %s rl, " " %s snp, " " mrnaRefseq mrs " "where snp.chrom = kg.chrom " " and kg.name = mrs.mrna " " and mrs.refSeq = rl.mrnaAcc " " and kg.txStart < snp.chromStart " " and kg.txEnd > snp.chromEnd " " and snp.name = '%s'",refLinkTable, table, name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("<BR><A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?"); printf("geneId=%s\" TARGET=_blank>Entrez Gene for ", row[0]); printf("%s</A><BR>\n", row[1]); } sqlFreeResult(&sr); } hFreeConn(&conn); } void doSnpOld(struct trackDb *tdb, char *itemName) /* Put up info on a SNP. */ { char *snpTable = tdb->table; struct snp snp; struct snpMap snpMap; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; char *printId; cartWebStart(cart, database, "Simple Nucleotide Polymorphism (SNP)"); printf("<H2>Simple Nucleotide Polymorphism (SNP) %s</H2>\n", itemName); sqlSafef(query, sizeof query, "select * " "from %s " "where chrom = '%s' " " and chromStart = %d " " and name = '%s'", snpTable, seqName, start, itemName); rowOffset = hOffsetPastBin(database, seqName, snpTable); sr = sqlGetResult(conn, query); if (sameString(snpTable,"snpMap")) while ((row = sqlNextRow(sr)) != NULL) { snpMapStaticLoad(row+rowOffset, &snpMap); bedPrintPos((struct bed *)&snpMap, 3, tdb); } else while ((row = sqlNextRow(sr)) != NULL) { snpStaticLoad(row+rowOffset, &snp); bedPrintPos((struct bed *)&snp, 3, tdb); } /* write dbSnpRs details if found. */ printId = doDbSnpRs(itemName); if (printId) { puts("<BR>"); if (sameString(printId, "valid")) { printDbSnpRsUrl(itemName, "dbSNP link"); putchar('\n'); doSnpEntrezGeneLink(tdb, itemName); } else { printDbSnpRsUrl(printId, "dbSNP link (%s)", printId); putchar('\n'); doSnpEntrezGeneLink(tdb, printId); } } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void writeSnpException(char *exceptionList, char *itemName, int rowOffset, char *chrom, int chromStart, struct trackDb *tdb) { char *tokens; struct lineFile *lf; struct tokenizer *tkz; struct snpExceptions se; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *id; char *br=" "; char *noteColor="#7f0000"; boolean firstException=TRUE; boolean multiplePositions=FALSE; if (sameString(exceptionList,"0")) return; tokens=cloneString(exceptionList); lf=lineFileOnString("snpExceptions", TRUE, tokens); tkz=tokenizerOnLineFile(lf); while ((id=tokenizerNext(tkz))!=NULL) { if (firstException) { printf("<BR><B style='color:%s;'>Note(s):</B><BR>\n",noteColor); firstException=FALSE; } if (sameString(id,",")) /* is there a tokenizer that doesn't return separators? */ continue; if (sameString(id,"18")||sameString(id,"19")||sameString(id,"20")) multiplePositions=TRUE; br=cloneString("<BR>"); sqlSafef(query, sizeof(query), "select * from snpExceptions where exceptionId = %s", id); sr = sqlGetResult(conn, query); /* exceptionId is a primary key; at most 1 record returned */ while ((row = sqlNextRow(sr))!=NULL) { snpExceptionsStaticLoad(row, &se); printf(" <B style='color:%s;'>%s</B><BR>\n", noteColor,se.description); } } printf("%s\n",br); if (multiplePositions) { struct snp snp; printf("<B style='color:#7f0000;'>Other Positions</B>:<BR><BR>"); sqlSafef(query, sizeof(query), "select * from snp where name='%s'", itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr))!=NULL) { snpStaticLoad(row+rowOffset, &snp); if (differentString(chrom,snp.chrom) || chromStart!=snp.chromStart) { bedPrintPos((struct bed *)&snp, 3, tdb); printf("<BR>\n"); } } } } void printSnpInfo(struct snp snp) /* print info on a snp */ { if (differentString(snp.strand,"?")) {printf("<B>Strand: </B>%s\n", snp.strand);} printf("<BR><B>Observed: </B>%s\n", snp.observed); printf("<BR><B><A HREF=\"#Source\">Source</A>: </B>%s\n", snp.source); printf("<BR><B><A HREF=\"#MolType\">Molecule Type</A>: </B>%s\n", snp.molType); printf("<BR><B><A HREF=\"#Class\">Variant Class</A>: </B>%s\n", snp.class); printf("<BR><B><A HREF=\"#Valid\">Validation Status</A>: </B>%s\n", snp.valid); printf("<BR><B><A HREF=\"#Func\">Function</A>: </B>%s\n", snp.func); printf("<BR><B><A HREF=\"#LocType\">Location Type</A>: </B>%s\n", snp.locType); if (snp.avHet>0) printf("<BR><B><A HREF=\"#AvHet\">Average Heterozygosity</A>: </B>%.3f +/- %.3f", snp.avHet, snp.avHetSE); printf("<BR>\n"); } off_t getSnpSeqFileOffset(struct trackDb *tdb, struct snp *snp) /* do a lookup in snpSeq for the offset */ { char *snpSeqSetting = trackDbSetting(tdb, "snpSeq"); char snpSeqTable[128]; char query[256]; char **row; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; off_t offset = 0; if (isNotEmpty(snpSeqSetting)) { if (hTableExists(database, snpSeqSetting)) safecpy(snpSeqTable, sizeof(snpSeqTable), snpSeqSetting); else return -1; } else { safef(snpSeqTable, sizeof(snpSeqTable), "%sSeq", tdb->table); if (!hTableExists(database, snpSeqTable)) { safecpy(snpSeqTable, sizeof(snpSeqTable), "snpSeq"); if (!hTableExists(database, snpSeqTable)) return -1; } } sqlSafef(query, sizeof(query), "select file_offset from %s where acc='%s'", snpSeqTable, snp->name); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) return -1; offset = sqlLongLong(row[0]); sqlFreeResult(&sr); hFreeConn(&conn); return offset; } char *getSnpSeqFile(struct trackDb *tdb, int version) /* find location of snp.fa and test existence. */ { char *seqFile = trackDbSetting(tdb, "snpSeqFile"); if (isNotEmpty(seqFile)) { if (fileExists(seqFile)) return cloneString(seqFile); else return NULL; } char seqFileBuf[512]; safef(seqFileBuf, sizeof(seqFileBuf), "/gbdb/%s/snp/%s.fa", database, tdb->table); if (fileExists(seqFileBuf)) return cloneString(seqFileBuf); safef(seqFileBuf, sizeof(seqFileBuf), "/gbdb/%s/snp/snp%d.fa", database, version); if (fileExists(seqFileBuf)) return cloneString(seqFileBuf); safef(seqFileBuf, sizeof(seqFileBuf), "/gbdb/%s/snp/snp.fa", database); if (fileExists(seqFileBuf)) return cloneString(seqFileBuf); return NULL; } void printNullAlignment(int l, int r, int q) /* Print out a double-sided gap for unaligned insertion SNP. */ { int digits = max(digitsBaseTen(r), digitsBaseTen(q)); printf("%0*d - %0*d\n" "%*s" " (dbSNP-annotated position was not re-aligned to " "observed allele code -- see adjacent alignments)\n" "%0*d - %0*d</B>\n\n", digits, l, digits, r, (digits*2 + 3), "", digits, q+1, digits, q); } void printOffsetAndBoldAxt(struct axt *axtIn, int lineWidth, struct axtScoreScheme *ss, int tOffset, int qOffset, int boldStart, int boldEnd, boolean tIsRc, int tSize, int qSize) /* Given an axt block, break it into multiple blocks for printing if * the bold range falls in the middle; add t & qOffset to t & q * coords; and print all blocks. boldStart and boldEnd are relative to * the target sequence used to make axtIn (start at 0, not tOffset). * tIsRc means that the target sequence that was aligned to create axtIn * was reverse-complemented so we want to display t coords backwards; * that includes reversing block coords within the target seq range. */ { struct axt axtBlock; int nullQStart = 0; /* (Defining a macro because a function would have an awful lot of arguments.) * First extract the portion of axtIn for this block. If tIsRc, then * reverse the block's t coords within the range of (0, tSize]. * Add t and qOffset, swap target and query so that target sequence is on top, * and print it out, adding bold tags before and afterwards if isBold. */ #define doBlock(blkStart, blkEnd, isBold) \ if (isBold) printf("<B>"); \ if (axtGetSubsetOnT(axtIn, &axtBlock, blkStart, blkEnd, ss, isBold)) \ { \ if (tIsRc) \ { \ int tmp = axtBlock.tStart; \ axtBlock.tStart = tSize - axtBlock.tEnd; \ axtBlock.tEnd = tSize - tmp; \ } \ axtBlock.tStart += tOffset; axtBlock.tEnd += tOffset; \ axtBlock.qStart += qOffset; axtBlock.qEnd += qOffset; \ nullQStart = axtBlock.qEnd; \ axtSwap(&axtBlock, tSize, qSize); \ axtPrintTraditionalExtra(&axtBlock, lineWidth, ss, stdout, \ FALSE, tIsRc); \ } \ else if (isBold) \ { \ int ins = (tIsRc ? tSize - blkEnd : blkEnd) + tOffset; \ int l = tIsRc ? ins : ins+1, r = tIsRc ? ins+1 : ins; \ printNullAlignment(l, r, nullQStart); \ } \ if (isBold) printf("</B>"); /* First block: before bold range */ doBlock(axtIn->tStart, boldStart, FALSE); /* Second block: bold range */ doBlock(boldStart, boldEnd, TRUE); /* Third block: after bold range */ doBlock(boldEnd, axtIn->tEnd, FALSE); #undef doBlock } void generateAlignment(struct dnaSeq *tSeq, struct dnaSeq *qSeq, int lineWidth, int tOffset, int qOffset, int boldStart, int boldEnd, boolean tIsRc) /* Use axtAffine to align tSeq to qSeq. Print the resulting alignment. * tOffset and qOffset are added to the respective sets of coordinates for * printing. If boldStart and boldEnd have any overlap with the aligned * tSeq, print that region as a separate block, in bold. boldStart and * boldEnd are relative to the start of tSeq (start at 0 not tOffset). * tIsRc means that tSeq has been reverse-complemented so we want to * display t coords backwards. */ { int matchScore = 100; int misMatchScore = 100; int gapOpenPenalty = 400; int gapExtendPenalty = 50; struct axtScoreScheme *ss = axtScoreSchemeSimpleDna(matchScore, misMatchScore, gapOpenPenalty, gapExtendPenalty); struct axt *axt = axtAffine(qSeq, tSeq, ss), *axtBlock=axt; hPrintf("<PRE>"); if (axt == NULL) { printf("%s and %s don't align\n", tSeq->name, qSeq->name); return; } printf("<B>Alignment between genome (%s, %c strand; %d bp) and " "dbSNP sequence (%s; %d bp)</B>\n", tSeq->name, (tIsRc ? '-' : '+'), tSeq->size, qSeq->name, qSeq->size); for (axtBlock=axt; axtBlock !=NULL; axtBlock = axtBlock->next) { printf("ID (including gaps) %3.1f%%, coverage (of both) %3.1f%%\n\n", axtIdWithGaps(axtBlock)*100, axtCoverage(axtBlock, qSeq->size, tSeq->size)*100); printOffsetAndBoldAxt(axtBlock, lineWidth, ss, tOffset, qOffset, boldStart, boldEnd, tIsRc, tSeq->size, qSeq->size); } axtFree(&axt); hPrintf("</PRE>"); } void printSnpAlignment(struct trackDb *tdb, struct snp *snp, int version) /* Get flanking sequences from table; align and print */ { char *fileName = NULL; char *variation = NULL; char *line; struct lineFile *lf = NULL; static int maxFlank = 1000; static int lineWidth = 100; boolean gotVar = FALSE; boolean leftFlankTrimmed = FALSE; boolean rightFlankTrimmed = FALSE; struct dyString *seqDbSnp5 = newDyString(512); struct dyString *seqDbSnp3 = newDyString(512); struct dyString *seqDbSnpTemp = newDyString(512); char *leftFlank = NULL; char *rightFlank = NULL; struct dnaSeq *dnaSeqDbSnp5 = NULL; struct dnaSeq *dnaSeqDbSnpO = NULL; struct dnaSeq *dnaSeqDbSnp3 = NULL; struct dnaSeq *seqDbSnp = NULL; struct dnaSeq *seqNib = NULL; int len5 = 0; int len3 = 0; int start = 0; int end = 0; int skipCount = 0; off_t offset = 0; fileName = getSnpSeqFile(tdb, version); if (!fileName) return; offset = getSnpSeqFileOffset(tdb, snp); if (offset == -1) return; lf = lineFileOpen(fileName, TRUE); lineFileSeek(lf, offset, SEEK_SET); /* skip the header line */ lineFileNext(lf, &line, NULL); if (!startsWith(">rs", line)) errAbort("Expected FASTA header, got this line:\n%s\nat offset %lld " "in file %s", line, (long long)offset, fileName); while (lineFileNext(lf, &line, NULL)) { stripString(line, " "); int len = strlen(line); if (len == 0) break; else if (len == 1 && isIupacAmbiguous(line[0])) { gotVar = TRUE; variation = cloneString(line); } else if (gotVar) dyStringAppend(seqDbSnp3, line); else dyStringAppend(seqDbSnp5, line); } lineFileClose(&lf); if (variation == NULL) { printf("<P>Could not parse ambiguous SNP base out of dbSNP " "sequence, so can't display re-alignment of flanking sequences.\n"); return; } /* trim */ /* axtAffine has a limit of 100,000,000 bases for query x target */ leftFlank = dyStringCannibalize(&seqDbSnp5); rightFlank = dyStringCannibalize(&seqDbSnp3); len5 = strlen(leftFlank); len3 = strlen(rightFlank); if (len5 > maxFlank) { skipCount = len5 - maxFlank; leftFlank = leftFlank + skipCount; leftFlankTrimmed = TRUE; len5 = strlen(leftFlank); } if (len3 > maxFlank) { rightFlank[maxFlank] = '\0'; rightFlankTrimmed = TRUE; len3 = strlen(rightFlank); } /* get genomic coords */ int isRc = sameString(snp->strand, "-"); if (isRc) { start = snp->chromStart - len3; end = snp->chromEnd + len5; } else { start = snp->chromStart - len5; end = snp->chromEnd + len3; } int genoLen3 = len3; int genoLen5 = len5; if (start < 0) { if (isRc) genoLen3 += start; else genoLen5 += start; start = 0; } int chromSize = hChromSize(database, snp->chrom); if (end > chromSize) { if (isRc) genoLen5 += (chromSize - end); else genoLen3 += (chromSize - end); end = chromSize; } /* do the lookup */ seqNib = hChromSeqMixed(database, snp->chrom, start, end); if (seqNib == NULL) errAbort("Couldn't get genomic sequence around %s (%s:%d-%d)", snp->name, snp->chrom, start+1, end); if (isRc) reverseComplement(seqNib->dna, seqNib->size); char betterName[512]; safef(betterName, sizeof(betterName), "%s %s:%d-%d", database, seqName, start+1, end); seqNib->name = cloneString(betterName); jsBeginCollapsibleSection(cart, tdb->track, "realignment", "Re-alignment of the SNP's flanking sequences to the genomic sequence", FALSE); printf("Note: this alignment was computed by UCSC and may not be identical to " "NCBI's alignment used to map the SNP.\n"); printf("<PRE><B>Genomic sequence around %s (%s:%d-%d, %s strand):</B>\n", snp->name, snp->chrom, start+1, end, isRc ? "reverse complemented for -" : "+"); int snpWidth = snp->chromEnd - snp->chromStart; writeSeqWithBreaks(stdout, seqNib->dna, genoLen5, lineWidth); printf("<B>"); if (snp->chromEnd > snp->chromStart) writeSeqWithBreaks(stdout, seqNib->dna + genoLen5, snpWidth, lineWidth); else printf("-\n"); printf("</B>"); writeSeqWithBreaks(stdout, seqNib->dna + seqNib->size - genoLen3, genoLen3, lineWidth); printf("</PRE>\n"); printf("\n<PRE><B>dbSNP flanking sequences and observed allele code for %s" ":</B>\n", snp->name); printf("(Uses "); printf("<A HREF=\"../goldenPath/help/iupac.html\"" ); printf("TARGET=_BLANK>IUPAC ambiguity codes</A>"); printf(")\n"); if (leftFlankTrimmed) printf("Left flank trimmed to %d bases.\n", maxFlank); if (rightFlankTrimmed) printf("Right flank trimmed to %d bases.\n", maxFlank); dnaSeqDbSnp5 = newDnaSeq(leftFlank, len5, "dbSNP seq 5"); dnaSeqDbSnpO = newDnaSeq(variation, strlen(variation),"dbSNP seq O"); dnaSeqDbSnp3 = newDnaSeq(rightFlank, len3, "dbSNP seq 3"); writeSeqWithBreaks(stdout, dnaSeqDbSnp5->dna, dnaSeqDbSnp5->size, lineWidth); printf("<B>"); writeSeqWithBreaks(stdout, dnaSeqDbSnpO->dna, dnaSeqDbSnpO->size, lineWidth); printf("</B>"); writeSeqWithBreaks(stdout, dnaSeqDbSnp3->dna, dnaSeqDbSnp3->size, lineWidth); printf("</PRE>\n"); /* create seqDbSnp */ dyStringAppend(seqDbSnpTemp, leftFlank); dyStringAppend(seqDbSnpTemp, variation); dyStringAppend(seqDbSnpTemp, rightFlank); seqDbSnp = newDnaSeq(seqDbSnpTemp->string, strlen(seqDbSnpTemp->string), snp->name); if (seqDbSnp == NULL) { warn("Couldn't get sequences"); return; } seqDbSnp->size = strlen(seqDbSnp->dna); generateAlignment(seqNib, seqDbSnp, lineWidth, start, skipCount, genoLen5, genoLen5 + snpWidth, isRc); jsEndCollapsibleSection(); } void doSnp(struct trackDb *tdb, char *itemName) /* Process SNP details. */ { char *snpTable = tdb->table; struct snp snp; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset=hOffsetPastBin(database, seqName, snpTable); int firstOne=1; char *exception=0; char *chrom=""; int chromStart=0; cartWebStart(cart, database, "Simple Nucleotide Polymorphism (SNP)"); printf("<H2>Simple Nucleotide Polymorphism (SNP) %s</H2>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom='%s' and " "chromStart=%d and name='%s'", snpTable, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr))!=NULL) { snpStaticLoad(row+rowOffset, &snp); if (firstOne) { exception=cloneString(snp.exception); chrom = cloneString(snp.chrom); chromStart = snp.chromStart; bedPrintPos((struct bed *)&snp, 3, tdb); printf("<BR>\n"); firstOne=0; } printSnpInfo(snp); } if (startsWith("rs",itemName)) { printDbSnpRsUrl(itemName, "dbSNP"); putchar('\n'); doSnpEntrezGeneLink(tdb, itemName); } if (hTableExists(database, "snpExceptions") && differentString(exception,"0")) writeSnpException(exception, itemName, rowOffset, chrom, chromStart, tdb); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doAffy120KDetails(struct trackDb *tdb, char *name) /* print additional SNP details */ { struct sqlConnection *conn = sqlConnect("hgFixed"); char query[1024]; struct affy120KDetails *snp = NULL; sqlSafef(query, sizeof(query), "select affyId, rsId, baseA, baseB, sequenceA, sequenceB, " " enzyme, minFreq, hetzyg, avHetSE, " " NA04477, NA04479, NA04846, NA11036, NA11038, NA13056, " " NA17011, NA17012, NA17013, NA17014, NA17015, NA17016, " " NA17101, NA17102, NA17103, NA17104, NA17105, NA17106, " " NA17201, NA17202, NA17203, NA17204, NA17205, NA17206, " " NA17207, NA17208, NA17210, NA17211, NA17212, NA17213, " " PD01, PD02, PD03, PD04, PD05, PD06, PD07, PD08, " " PD09, PD10, PD11, PD12, PD13, PD14, PD15, PD16, " " PD17, PD18, PD19, PD20, PD21, PD22, PD23, PD24 " "from affy120KDetails " "where affyId = %s", name); snp = affy120KDetailsLoadByQuery(conn, query); if (snp!=NULL) { printf("<BR>\n"); printf("<B>Sample Prep Enzyme:</B> <I>%s</I><BR>\n",snp->enzyme); printf("<B>Minimum Allele Frequency:</B> %.3f<BR>\n",snp->minFreq); printf("<B>Heterozygosity:</B> %.3f<BR>\n",snp->hetzyg); printf("<B>Base A: </B> <span style='font-family:Courier;'>%s</span><BR>\n", snp->baseA); printf("<B>Base B: </B> <span style='font-family:Courier;'>%s</span><BR>\n", snp->baseB); printf("<B>Sequence of Allele A:</B> <span style='font-family:Courier;'>"); printf("%s</span><BR>\n",snp->sequenceA); printf("<B>Sequence of Allele B:</B> <span style='font-family:Courier;'>"); printf("%s</span><BR>\n",snp->sequenceB); if (isNotEmpty(snp->rsId)) { puts("<BR>"); printDbSnpRsUrl(snp->rsId, "dbSNP link for %s", snp->rsId); puts("<BR>"); } doSnpEntrezGeneLink(tdb, snp->rsId); printf("<BR>Genotypes:<BR>"); printf("\n<BR><span style='font-family:Courier;'>"); printf("NA04477: %s ", snp->NA04477); printf("NA04479: %s ", snp->NA04479); printf("NA04846: %s ", snp->NA04846); printf("NA11036: %s ", snp->NA11036); printf("NA11038: %s ", snp->NA11038); printf("NA13056: %s ", snp->NA13056); printf("\n<BR>NA17011: %s ", snp->NA17011); printf("NA17012: %s ", snp->NA17012); printf("NA17013: %s ", snp->NA17013); printf("NA17014: %s ", snp->NA17014); printf("NA17015: %s ", snp->NA17015); printf("NA17016: %s ", snp->NA17016); printf("\n<BR>NA17101: %s ", snp->NA17101); printf("NA17102: %s ", snp->NA17102); printf("NA17103: %s ", snp->NA17103); printf("NA17104: %s ", snp->NA17104); printf("NA17105: %s ", snp->NA17105); printf("NA17106: %s ", snp->NA17106); printf("\n<BR>NA17201: %s ", snp->NA17201); printf("NA17202: %s ", snp->NA17202); printf("NA17203: %s ", snp->NA17203); printf("NA17204: %s ", snp->NA17204); printf("NA17205: %s ", snp->NA17205); printf("NA17206: %s ", snp->NA17206); printf("\n<BR>NA17207: %s ", snp->NA17207); printf("NA17208: %s ", snp->NA17208); printf("NA17210: %s ", snp->NA17210); printf("NA17211: %s ", snp->NA17211); printf("NA17212: %s ", snp->NA17212); printf("NA17213: %s ", snp->NA17213); printf("\n<BR>PD01: %s ", snp->PD01); printf("PD02: %s ", snp->PD02); printf("PD03: %s ", snp->PD03); printf("PD04: %s ", snp->PD04); printf("PD05: %s ", snp->PD05); printf("PD06: %s ", snp->PD06); printf("\n<BR>PD07: %s ", snp->PD07); printf("PD08: %s ", snp->PD08); printf("PD09: %s ", snp->PD09); printf("PD10: %s ", snp->PD10); printf("PD11: %s ", snp->PD11); printf("PD12: %s ", snp->PD12); printf("\n<BR>PD13: %s ", snp->PD13); printf("PD14: %s ", snp->PD14); printf("PD15: %s ", snp->PD15); printf("PD16: %s ", snp->PD16); printf("PD17: %s ", snp->PD17); printf("PD18: %s ", snp->PD18); printf("\n<BR>PD19: %s ", snp->PD19); printf("PD20: %s ", snp->PD20); printf("PD21: %s ", snp->PD21); printf("PD22: %s ", snp->PD22); printf("PD23: %s ", snp->PD23); printf("PD24: %s ", snp->PD24); printf("\n</span>\n"); } affy120KDetailsFree(&snp); sqlDisconnect(&conn); } void doCnpLocke(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpLocke thisItem; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); printf("<B>NCBI Clone Registry: </B><A href="); printCloneDbUrl(stdout, itemName); printf(" target=_blank>%s</A><BR>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpLockeStaticLoad(row+rowOffset, &thisItem); bedPrintPos((struct bed *)&thisItem, 3, tdb); printf("<BR><B>Variation Type</B>: %s\n",thisItem.variationType); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doCnpIafrate(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpIafrate cnpIafrate; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); printf("<B>NCBI Clone Registry: </B><A href="); printCloneDbUrl(stdout, itemName); printf(" target=_blank>%s</A><BR>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpIafrateStaticLoad(row+rowOffset, &cnpIafrate); bedPrintPos((struct bed *)&cnpIafrate, 3, tdb); printf("<BR><B>Variation Type</B>: %s\n",cnpIafrate.variationType); printf("<BR><B>Score</B>: %g\n",cnpIafrate.score); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doCnpIafrate2(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpIafrate2 thisItem; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); printf("<B>NCBI Clone Registry: </B><A href="); printCloneDbUrl(stdout, itemName); printf(" target=_blank>%s</A><BR>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpIafrate2StaticLoad(row+rowOffset, &thisItem); bedPrintPos((struct bed *)&thisItem, 3, tdb); printf("<BR><B>Cohort Type</B>: %s\n",thisItem.cohortType); if (strstr(thisItem.cohortType, "Control")) { printf("<BR><B>Control Gain Count</B>: %d\n",thisItem.normalGain); printf("<BR><B>Control Loss Count</B>: %d\n",thisItem.normalLoss); } if (strstr(thisItem.cohortType, "Patient")) { printf("<BR><B>Patient Gain Count</B>: %d\n",thisItem.patientGain); printf("<BR><B>Patient Loss Count</B>: %d\n",thisItem.patientLoss); } } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doDelHinds2(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct delHinds2 thisItem; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { delHinds2StaticLoad(row+rowOffset, &thisItem); bedPrintPos((struct bed *)&thisItem, 3, tdb); printf("<BR><B>Frequency</B>: %3.2f%%\n",thisItem.frequency); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doDelConrad2(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct delConrad2 thisItem; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { delConrad2StaticLoad(row+rowOffset, &thisItem); bedPrintPos((struct bed *)&thisItem, 3, tdb); printf("<BR><B>HapMap individual</B>: %s\n",thisItem.offspring); printf("<BR><B>HapMap population</B>: %s\n",thisItem.population); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doCnpSebat(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpSebat cnpSebat; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpSebatStaticLoad(row+rowOffset, &cnpSebat); bedPrintPos((struct bed *)&cnpSebat, 3, tdb); printf("<BR><B>Number of probes</B>: %d\n",cnpSebat.probes); printf("<BR><B>Number of individuals</B>: %d\n",cnpSebat.individuals); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doCnpSebat2(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpSebat2 cnpSebat2; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpSebat2StaticLoad(row+rowOffset, &cnpSebat2); bedPrintPos((struct bed *)&cnpSebat2, 3, tdb); printf("<BR><B>Number of probes</B>: %d\n",cnpSebat2.probes); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void printCnpSharpDetails(struct cnpSharp cnpSharp) { printf("<B>Name: </B> %s <BR>\n", cnpSharp.name); printf("<B>Variation type: </B> %s <BR>\n", cnpSharp.variationType); printf("<B>Cytoband: </B> %s <BR>\n", cnpSharp.cytoName); printf("<B>Strain: </B> %s <BR>\n", cnpSharp.cytoStrain); printf("<B>Duplication Percent:</B> %.1f %%<BR>\n", cnpSharp.dupPercent*100); printf("<B>Repeat Percent: </B> %.1f %%<BR>\n", cnpSharp.repeatsPercent*100); printf("<B>LINE Percent: </B> %.1f %%<BR>\n", cnpSharp.LINEpercent*100); printf("<B>SINE Percent: </B> %.1f %%<BR>\n", cnpSharp.SINEpercent*100); printf("<B>LTR Percent: </B> %.1f %%<BR>\n", cnpSharp.LTRpercent*100); printf("<B>DNA Percent: </B> %.1f %%<BR>\n", cnpSharp.DNApercent*100); printf("<B>Disease Percent: </B> %.1f %%<BR>\n", cnpSharp.diseaseSpotsPercent*100); } void printCnpSharpSampleData(char *itemName) { struct sqlConnection *hgFixed1 = sqlConnect("hgFixed"); struct sqlConnection *hgFixed2 = sqlConnect("hgFixed"); char query[256], query2[1024]; char **row; struct sqlResult *sr1, *sr2; float sample, cutoff; printf("<BR>\n"); sqlSafef(query, sizeof(query), "select distinct substring(sample,1,5) from cnpSharpCutoff order by sample"); sr1 = sqlGetResult(hgFixed1, query); while ((row = sqlNextRow(sr1)) != NULL) { char *pop=row[0]; printf("<table border=\"1\" cellpadding=\"0\" ><tr>"); sqlSafef(query2, sizeof(query2), "select s1.sample, s1.gender, s1.value, c1.value, s2.value, c2.value " "from cnpSharpSample s1, cnpSharpSample s2, cnpSharpCutoff c1, cnpSharpCutoff c2 " "where s1.sample=s2.sample and s1.sample=c1.sample and s1.sample=c2.sample " " and s1.batch=1 and s2.batch=2 and c1.batch=1 and c2.batch=2 and s1.bac='%s' " " and s1.bac=s2.bac and s1.sample like '%s%%' order by s1.sample", itemName, pop); sr2 = sqlGetResult(hgFixed2, query2); while ((row = sqlNextRow(sr2)) != NULL) { if (sameString(row[1],"M")) printf("<TD width=160 bgcolor=\"#99FF99\">"); else printf("<TD width=160 bgcolor=\"#FFCCFF\">"); printf("%s</TD>\n",row[0]); } printf("</TR><TR>\n"); sqlFreeResult(&sr2); sr2 = sqlGetResult(hgFixed2, query2); while ((row = sqlNextRow(sr2)) != NULL) { sample = sqlFloat(row[2]); cutoff = sqlFloat(row[3]); if (sameString(row[2],"NA")) printf("<TD width=160 > NA / %.3f </TD>\n",cutoff); else if (sample>=cutoff) printf("<TD width=160 bgcolor=\"yellow\"> %.3f / %.3f </TD>\n",sample,cutoff); else if (sample<= 0-cutoff) printf("<TD width=160 bgcolor=\"gray\"> %.3f / -%.3f </TD>\n",sample,cutoff); else printf("<TD width=160 > %.3f / %.3f </TD>\n",sample,cutoff); } printf("</TR><TR>\n"); sqlFreeResult(&sr2); sr2 = sqlGetResult(hgFixed2, query2); while ((row = sqlNextRow(sr2)) != NULL) { sample = sqlFloat(row[4]); cutoff = sqlFloat(row[5]); if (sameString(row[4],"NA")) printf("<TD width=160 > NA / %.3f </TD>\n",cutoff); else if (sample>=cutoff) printf("<TD width=160 bgcolor=\"yellow\"> %.3f / %.3f </TD>\n",sample,cutoff); else if (sample<= 0-cutoff) printf("<TD width=160 bgcolor=\"gray\"> %.3f / -%.3f </TD>\n",sample,cutoff); else printf("<TD width=160 > %.3f / %.3f </TD>\n",sample,cutoff); } sqlFreeResult(&sr2); printf("</tr></table>\n"); } sqlFreeResult(&sr1); hFreeConn(&hgFixed1); hFreeConn(&hgFixed2); printf("<BR><B>Legend for individual values in table:</B>\n"); printf(" <table>"); printf("<TR><TD>Title Color:</TD><TD bgcolor=\"#FFCCFF\">Female</TD><TD bgcolor=\"#99FF99\">Male</TD></TR>\n"); printf("<TR><TD>Value Color:</TD><TD bgcolor=\"yellow\" >Above Threshold</TD><TD bgcolor=\"gray\">Below negative threshold</TD></TR>\n"); printf("<TR><TD>Data Format:</TD><TD>Value / Threshold</TD></TR>\n"); printf("</table>\n"); } void doCnpSharp(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpSharp cnpSharp; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); char variantSignal; char *itemCopy = cloneString(itemName); variantSignal = lastChar(itemName); if (variantSignal == '*') stripChar(itemCopy, '*'); if (variantSignal == '?') stripChar(itemCopy, '?'); if (variantSignal == '#') stripChar(itemCopy, '#'); genericHeader(tdb, itemCopy); printf("<B>NCBI Clone Registry: </B><A href="); printCloneDbUrl(stdout, itemCopy); printf(" target=_blank>%s</A><BR>\n", itemCopy); if (variantSignal == '*' || variantSignal == '?' || variantSignal == '#') printf("<B>Note this BAC was found to be variant. See references.</B><BR>\n"); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpSharpStaticLoad(row+rowOffset, &cnpSharp); bedPrintPos((struct bed *)&cnpSharp, 3, tdb); printCnpSharpDetails(cnpSharp); } sqlFreeResult(&sr); hFreeConn(&conn); // printCnpSharpSampleData(itemName); printTrackHtml(tdb); } void doCnpSharp2(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct cnpSharp2 cnpSharp2; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); printf("<B>NCBI Clone Registry: </B><A href="); printCloneDbUrl(stdout, itemName); printf(" target=_blank>%s</A><BR>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cnpSharp2StaticLoad(row+rowOffset, &cnpSharp2); bedPrintPos((struct bed *)&cnpSharp2, 3, tdb); printf("<B>Name: </B> %s <BR>\n", cnpSharp2.name); printf("<B>Variation type: </B> %s <BR>\n", cnpSharp2.variationType); } sqlFreeResult(&sr); hFreeConn(&conn); // printCnpSharpSampleData(itemName); printTrackHtml(tdb); } void doDgv(struct trackDb *tdb, char *id) /* Details for Database of Genomic Variants (updated superset of cnp*). */ { struct dgv dgv; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[512]; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb, id); printCustomUrl(tdb, id, FALSE); sqlSafef(query, sizeof(query), "select * from %s where name = '%s' " "and chrom = '%s' and chromStart = %d and chromEnd = %d", tdb->table, id, seqName, start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { dgvStaticLoad(row+rowOffset, &dgv); if (dgv.chromStart != dgv.thickStart || (dgv.chromEnd != dgv.thickEnd && dgv.thickEnd != dgv.chromStart)) { printf("<B>Variant Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A><BR>\n", hgTracksPathAndSettings(), database, dgv.chrom, dgv.thickStart+1, dgv.thickEnd, dgv.chrom, dgv.thickStart+1, dgv.thickEnd); printBand(dgv.chrom, dgv.thickStart, dgv.thickEnd, FALSE); printf("<B>Variant Genomic Size:</B> %d<BR>\n", dgv.thickEnd - dgv.thickStart); printf("<B>Locus:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A><BR>\n", hgTracksPathAndSettings(), database, dgv.chrom, dgv.chromStart+1, dgv.chromEnd, dgv.chrom, dgv.chromStart+1, dgv.chromEnd); printf("<B>Locus Genomic Size:</B> %d<BR>\n", dgv.chromEnd - dgv.chromStart); } else { printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A><BR>\n", hgTracksPathAndSettings(), database, dgv.chrom, dgv.chromStart+1, dgv.chromEnd, dgv.chrom, dgv.chromStart+1, dgv.chromEnd); printBand(dgv.chrom, dgv.chromStart, dgv.chromEnd, FALSE); printf("<B>Genomic Size:</B> %d<BR>\n", dgv.chromEnd - dgv.chromStart); } printf("<B>Variant Type:</B> %s<BR>\n", dgv.varType); printf("<B>Reference:</B> <A HREF=\""); printEntrezPubMedUidAbstractUrl(stdout, dgv.pubMedId); printf("\" TARGET=_BLANK>%s</A><BR>\n", dgv.reference); printf("<B>Method/platform:</B> %s<BR>\n", dgv.method); printf("<B>Sample:</B> %s<BR>\n", dgv.sample); if (isNotEmpty(dgv.landmark)) printf("<B>Landmark:</B> %s<BR>\n", dgv.landmark); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } static void maybePrintCoriellLinks(struct trackDb *tdb, char *commaSepIds) /* If id looks like a Coriell NA ID, print a link to Coriell, otherwise just print id. */ { char *coriellUrlBase = trackDbSetting(tdb, "coriellUrlBase"); struct slName *id, *sampleIds = slNameListFromComma(commaSepIds); for (id = sampleIds; id != NULL; id = id->next) { if (startsWith("NA", id->name) && countLeadingDigits(id->name+2) == strlen(id->name+2) && isNotEmpty(coriellUrlBase)) { // I don't know why coriell doesn't have direct links to NA's but oh well, // we can substitute 'GM' for 'NA' to get to the page... char *gmId = cloneString(id->name); gmId[0] = 'G'; gmId[1] = 'M'; printf("<A HREF=\"%s%s\" TARGET=_BLANK>%s</A>", coriellUrlBase, gmId, id->name); freeMem(gmId); } else printf("%s", id->name); if (id->next != NULL) printf(", "); } slNameFreeList(&sampleIds); } static void printBrowserPosLinks(char *commaSepIds) /* Print hgTracks links with position=id. */ { struct slName *id, *sampleIds = slNameListFromComma(commaSepIds); for (id = sampleIds; id != NULL; id = id->next) { char *searchTerm = cgiEncode(trimSpaces(id->name)); printf("<A HREF=\"%s&position=%s\">%s</A>", hgTracksPathAndSettings(), searchTerm, id->name); if (id->next != NULL) printf(", "); freeMem(searchTerm); } slNameFreeList(&sampleIds); } void doDgvPlus(struct trackDb *tdb, char *id) /* Details for Database of Genomic Variants, July 2013 and later. */ { struct dgvPlus dgv; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[512]; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb, id); printCustomUrl(tdb, id, FALSE); sqlSafef(query, sizeof(query), "select * from %s where name = '%s' " "and chrom = '%s' and chromStart = %d and chromEnd = %d", tdb->table, id, seqName, start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { dgvPlusStaticLoad(row+rowOffset, &dgv); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A><BR>\n", hgTracksPathAndSettings(), database, dgv.chrom, dgv.chromStart+1, dgv.chromEnd, dgv.chrom, dgv.chromStart+1, dgv.chromEnd); printBand(dgv.chrom, dgv.chromStart, dgv.chromEnd, FALSE); printf("<B>Genomic size:</B> %d<BR>\n", dgv.chromEnd - dgv.chromStart); printf("<B>Variant type:</B> %s<BR>\n", dgv.varType); printf("<B>Reference:</B> <A HREF=\""); printEntrezPubMedUidAbstractUrl(stdout, dgv.pubMedId); printf("\" TARGET=_BLANK>%s</A><BR>\n", dgv.reference); printf("<B>Method:</B> %s<BR>\n", dgv.method); if (isNotEmpty(dgv.platform)) printf("<B>Platform:</B> %s<BR>\n", dgv.platform); if (isNotEmpty(dgv.cohortDescription)) printf("<B>Sample cohort description:</B> %s<BR>\n", dgv.cohortDescription); if (isNotEmpty(dgv.samples)) { printf("<B>Sample IDs:</B> "); maybePrintCoriellLinks(tdb, dgv.samples); printf("<BR>\n"); } printf("<B>Sample size:</B> %u<BR>\n", dgv.sampleSize); if (dgv.observedGains != 0 || dgv.observedLosses != 0) { printf("<B>Observed gains:</B> %u<BR>\n", dgv.observedGains); printf("<B>Observed losses:</B> %u<BR>\n", dgv.observedLosses); } if (isNotEmpty(dgv.mergedVariants)) { printf("<B>Merged variants:</B> "); printBrowserPosLinks(dgv.mergedVariants); printf("<BR>\n"); } if (isNotEmpty(dgv.supportingVariants)) { printf("<B>Supporting variants:</B> "); printBrowserPosLinks(dgv.supportingVariants); printf("<BR>\n"); } if (isNotEmpty(dgv.genes)) { printf("<B>Genes:</B> "); printBrowserPosLinks(dgv.genes); printf("<BR>\n"); } } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doAffy120K(struct trackDb *tdb, char *itemName) /* Put up info on an Affymetrix SNP. */ { char *table = tdb->table; struct snp snp; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; cartWebStart(cart, database, "Single Nucleotide Polymorphism (SNP)"); printf("<H2>Single Nucleotide Polymorphism (SNP) %s</H2>\n", itemName); sqlSafef(query, sizeof query, "select * " "from affy120K " "where chrom = '%s' " " and chromStart = %d " " and name = '%s'", seqName, start, itemName); rowOffset = hOffsetPastBin(database, seqName, table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { snpStaticLoad(row+rowOffset, &snp); bedPrintPos((struct bed *)&snp, 3, tdb); } doAffy120KDetails(tdb, itemName); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doAffy10KDetails(struct trackDb *tdb, char *name) /* print additional SNP details */ { struct sqlConnection *conn = sqlConnect("hgFixed"); char query[1024]; struct affy10KDetails *snp=NULL; sqlSafef(query, sizeof(query), "select affyId, rsId, tscId, baseA, baseB, " "sequenceA, sequenceB, enzyme " /** minFreq, hetzyg, and avHetSE are waiting for additional data from Affy **/ /* " , minFreq, hetzyg, avHetSE "*/ "from affy10KDetails " "where affyId = '%s'", name); snp = affy10KDetailsLoadByQuery(conn, query); if (snp!=NULL) { printf("<BR>\n"); printf("<B>Sample Prep Enzyme: </B> <I>XbaI</I><BR>\n"); /** minFreq, hetzyg, and avHetSE are waiting for additional data from Affy **/ /* printf("<B>Minimum Allele Frequency:</B> %.3f<BR>\n",snp->minFreq);*/ /* printf("<B>Heterozygosity: </B> %.3f<BR>\n",snp->hetzyg);*/ /* printf("<B>Average Heterozygosity: </B> %.3f<BR>\n",snp->avHetSE);*/ printf("<B>Base A: </B> <span style='font-family:Courier;'>"); printf("%s</span><BR>\n",snp->baseA); printf("<B>Base B: </B> <span style='font-family:Courier;'>"); printf("%s</span><BR>\n",snp->baseB); printf("<B>Sequence of Allele A: </B> <span style='font-family:Courier;'>"); printf("%s</span><BR>\n",snp->sequenceA); printf("<B>Sequence of Allele B: </B> <span style='font-family:Courier;'>"); printf("%s</span><BR>\n",snp->sequenceB); printf("<P><A HREF=\"https://www.affymetrix.com/LinkServlet?probeset="); printf("%s", snp->affyId); printf("\" TARGET=_blank>Affymetrix NetAffx Analysis Center link for "); printf("%s</A></P>\n", snp->affyId); if (strncmp(snp->rsId,"unmapped",8)) { puts("<P>"); printDbSnpRsUrl(snp->rsId, "dbSNP link for %s", snp->rsId); puts("</P>"); } printf("<BR><A HREF=\"http://snp.cshl.org/cgi-bin/snp?name="); printf("%s\" TARGET=_blank>TSC link for %s</A>\n", snp->tscId, snp->tscId); doSnpEntrezGeneLink(tdb, snp->rsId); } /* else errAbort("<BR>Error in Query:\n%s<BR>\n",query); */ affy10KDetailsFree(&snp); sqlDisconnect(&conn); } void doAffy10K(struct trackDb *tdb, char *itemName) /* Put up info on an Affymetrix SNP. */ { char *table = tdb->table; struct snp snp; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset; cartWebStart(cart, database, "Single Nucleotide Polymorphism (SNP)"); printf("<H2>Single Nucleotide Polymorphism (SNP) %s</H2>\n", itemName); sqlSafef(query, sizeof query, "select * " "from affy10K " "where chrom = '%s' " " and chromStart = %d " " and name = '%s'", seqName, start, itemName); rowOffset = hOffsetPastBin(database, seqName, table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { snpStaticLoad(row+rowOffset, &snp); bedPrintPos((struct bed *)&snp, 3, tdb); } doAffy10KDetails(tdb, itemName); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void printSnpOrthoSummary(struct trackDb *tdb, char *rsId, char *observed) /* helper function for printSnp125Info */ { char *orthoTable = snp125OrthoTable(tdb, NULL); if (isNotEmpty(orthoTable) && hTableExists(database, orthoTable)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[512]; sqlSafef(query, sizeof(query), "select chimpAllele from %s where name='%s'", orthoTable, rsId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("<B>Summary: </B>%s>%s (chimp allele displayed first, " "then '>', then human alleles)<br>\n", row[0], observed); sqlFreeResult(&sr); hFreeConn(&conn); } } #define FOURBLANKCELLS "<TD></TD><TD></TD><TD></TD><TD></TD>" static char *abbreviateAllele(char *allele) /* If allele is >50bp then return an abbreviated version with first & last 20 bases and length; * otherwise just return (cloned) allele. */ { int length = strlen(allele); if (length > 50) { struct dyString *dyAbbr = dyStringCreate("%.20s", allele); dyStringAppend(dyAbbr, "..."); dyStringAppend(dyAbbr, allele+length - 20); dyStringPrintf(dyAbbr, " (%d bases)", length); return dyStringCannibalize(&dyAbbr); } return cloneString(allele); } void printSnpAlleleRows(struct snp125 *snp, int version) /* Print the UCSC ref allele (and dbSNP if it differs), as row(s) of a * 6-column table. */ { if (sameString(snp->strand,"+") || strchr(snp->refUCSC, '(')) // don't try to revComp refUCSC if it is "(N bp insertion)" etc. { printf("<TR><TD><B>Reference allele: </B></TD>" "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(snp->refUCSC)); if (!sameString(snp->refUCSC, snp->refNCBI)) printf("<TR><TD><B>dbSnp reference allele: </B></TD>" "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(snp->refNCBI)); } else if (sameString(snp->strand,"-")) { char *refUCSCRevComp = cloneString(snp->refUCSC); reverseComplement(refUCSCRevComp, strlen(refUCSCRevComp)); printf("<TR><TD><B>Reference allele: </B></TD>" "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(refUCSCRevComp)); if (version < 127 && !sameString(refUCSCRevComp, snp->refNCBI)) printf("<TR><TD><B>dbSnp reference allele: </B></TD>" "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(snp->refNCBI)); else if (version >= 127 && !sameString(snp->refUCSC, snp->refNCBI)) { char *refNCBIRevComp = cloneString(snp->refNCBI); if (! strchr(snp->refNCBI, '(')) reverseComplement(refNCBIRevComp, strlen(refNCBIRevComp)); printf("<TR><TD><B>dbSnp reference allele: </B></TD>" "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(refNCBIRevComp)); } } } #define TINYPADDING 3 void printSnpOrthoOneRow(char *orthoName, char *orthoDb, char *orthoAllele, char *orthoStrand, char *orthoChrom, int orthoStart, int orthoEnd) /* Print out a 6-column table row describing an orthologous allele. */ { printf("<TR><TD><B>%s allele: </B></TD>" "<TD align=center>%s</TD>\n", orthoName, orthoAllele); if (!sameString(orthoAllele, "?")) { printf("<TD> <B>%s strand: </B></TD>" "<TD>%s</TD>\n", orthoName, orthoStrand); printf("<TD> <B>%s position: </B></TD>" "<TD>\n", orthoName); if (isNotEmpty(orthoDb)) linkToOtherBrowser(orthoDb, orthoChrom, orthoStart-TINYPADDING, orthoEnd+TINYPADDING); printf("%s:%d-%d\n", orthoChrom, orthoStart+1, orthoEnd); printf("%s</TD>\n", isNotEmpty(orthoDb) ? "</A>" : ""); } else printf(FOURBLANKCELLS"\n"); printf("</TR>\n"); } void printSnpOrthoRows(struct trackDb *tdb, struct snp125 *snp) /* If a chimp+macaque ortho table was specified, print out the orthos * (if any), as rows of a 6-column table. */ { int speciesCount = 0; char *orthoTable = snp125OrthoTable(tdb, &speciesCount); if (isNotEmpty(orthoTable) && hTableExists(database, orthoTable)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[1024]; if (speciesCount == 2) sqlSafef(query, sizeof(query), "select chimpChrom, chimpStart, chimpEnd, chimpAllele, chimpStrand, " "macaqueChrom, macaqueStart, macaqueEnd, macaqueAllele, macaqueStrand " "from %s where chrom='%s' and bin=%d and chromStart=%d and name='%s'", orthoTable, seqName, binFromRange(snp->chromStart, snp->chromEnd), snp->chromStart, snp->name); else sqlSafef(query, sizeof(query), "select chimpChrom, chimpStart, chimpEnd, chimpAllele, chimpStrand, " "orangChrom, orangStart, orangEnd, orangAllele, orangStrand, " "macaqueChrom, macaqueStart, macaqueEnd, macaqueAllele, macaqueStrand " "from %s where chrom='%s' and bin=%d and chromStart=%d and name='%s'", orthoTable, seqName, binFromRange(snp->chromStart, snp->chromEnd), snp->chromStart, snp->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { char *chimpChrom = row[0]; int chimpStart = sqlUnsigned(row[1]); int chimpEnd = sqlUnsigned(row[2]); char *chimpAllele = row[3]; char *chimpStrand = row[4]; char *chimpDb = trackDbSetting(tdb, "chimpDb"); printSnpOrthoOneRow("Chimp", chimpDb, chimpAllele, chimpStrand, chimpChrom, chimpStart, chimpEnd); char *orangChrom, *orangAllele, *orangStrand, *orangDb; int orangStart, orangEnd; char *macaqueChrom, *macaqueAllele, *macaqueStrand, *macaqueDb; int macaqueStart, macaqueEnd; if (speciesCount == 2) { macaqueChrom = row[5]; macaqueStart = sqlUnsigned(row[6]); macaqueEnd = sqlUnsigned(row[7]); macaqueAllele = row[8]; macaqueStrand = row[9]; macaqueDb = trackDbSetting(tdb, "macaqueDb"); } else { orangChrom = row[5]; orangStart = sqlUnsigned(row[6]); orangEnd = sqlUnsigned(row[7]); orangAllele = row[8]; orangStrand = row[9]; orangDb = trackDbSetting(tdb, "orangDb"); printSnpOrthoOneRow("Orangutan", orangDb, orangAllele, orangStrand, orangChrom, orangStart, orangEnd); macaqueChrom = row[10]; macaqueStart = sqlUnsigned(row[11]); macaqueEnd = sqlUnsigned(row[12]); macaqueAllele = row[13]; macaqueStrand = row[14]; macaqueDb = trackDbSetting(tdb, "macaqueDb"); } printSnpOrthoOneRow("Macaque", macaqueDb, macaqueAllele, macaqueStrand, macaqueChrom, macaqueStart, macaqueEnd); sqlFreeResult(&sr); hFreeConn(&conn); } } } void printSnpAlleleAndOrthos(struct trackDb *tdb, struct snp125 *snp, int version) /* Print the UCSC ref allele (and dbSNP if it differs). If a * chimp+macaque ortho table was specified, print out the orthos (if * any). Wrap a table around them all so that if there are dbSNP, * chimp and/or macaque alleles, we can line them up nicely with the * reference allele. */ { printf("<TABLE border=0 cellspacing=0 cellpadding=0>\n"); printSnpAlleleRows(snp, version); printSnpOrthoRows(tdb, snp); printf("</TABLE>"); } static char getSnpTxBase(struct genePred *gene, int exonIx, int snpStart, int offset) /* Find the reference assembly base that is offset bases from snpStart in the translated sequence * of the gene. */ // Room for improvement: check for mRNA sequence associated with this gene, and use it if exists. { char base = 'N'; boolean ranOffEnd = FALSE; int i; int snpPlusOffset = snpStart; if (offset >= 0) { int exonEnd = gene->exonEnds[exonIx]; for (i = 0; i < offset; i++) { snpPlusOffset++; if (exonEnd <= snpPlusOffset) { if (++exonIx < gene->exonCount) { exonEnd = gene->exonEnds[exonIx]; snpPlusOffset = gene->exonStarts[exonIx]; } else ranOffEnd = TRUE; } } } else { int exonStart = gene->exonStarts[exonIx]; for (i = 0; i > offset; i--) { snpPlusOffset--; if (exonStart > snpPlusOffset) { if (--exonIx >= 0) { exonStart = gene->exonStarts[exonIx]; snpPlusOffset = gene->exonEnds[exonIx] - 1; } else ranOffEnd = TRUE; } } } if (! ranOffEnd) { struct dnaSeq *seq = hDnaFromSeq(database, gene->chrom, snpPlusOffset, snpPlusOffset+1, dnaUpper); base = seq->dna[0]; } return base; } char *getSymbolForGeneName(char *geneTable, char *geneId) /* Given a gene track and gene accession, look up the symbol if we know where to look * and if we find it, return a string with both symbol and acc. */ { struct dyString *dy = dyStringNew(32); char buf[256]; char *sym = NULL; if (sameString(geneTable, "knownGene") || sameString(geneTable, "refGene")) { struct sqlConnection *conn = hAllocConn(database); char query[256]; query[0] = '\0'; if (sameString(geneTable, "knownGene")) sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgID = '%s'", geneId); else if (sameString(geneTable, "refGene")) sqlSafef(query, sizeof(query), "select name from %s where mrnaAcc = '%s'", refLinkTable, geneId); sym = sqlQuickQuery(conn, query, buf, sizeof(buf)-1); hFreeConn(&conn); } if (sym != NULL) dyStringPrintf(dy, "%s (%s)", sym, geneId); else dyStringAppend(dy, geneId); return dyStringCannibalize(&dy); } #define firstTwoColumnsPctS "<TR><TD>%s </TD><TD>%s </TD><TD>" void getSnp125RefCodonAndSnpPos(struct snp125 *snp, struct genePred *gene, int exonIx, int *pSnpCodonPos, char refCodon[4], char *pRefAA) /* Given a single-base snp and a coding gene/exon containing it, determine the snp's position * in the codon and the reference codon & amino acid. */ { boolean geneIsRc = sameString(gene->strand, "-"); int snpStart = snp->chromStart, snpEnd = snp->chromEnd; int exonStart = gene->exonStarts[exonIx], exonEnd = gene->exonEnds[exonIx]; int cdsStart = gene->cdsStart, cdsEnd = gene->cdsEnd; int exonFrame = gene->exonFrames[exonIx]; if (exonFrame == -1) exonFrame = 0; if (cdsEnd < exonEnd) exonEnd = cdsEnd; if (cdsStart > exonStart) exonStart = cdsStart; int snpCodonPos = geneIsRc ? (2 - ((exonEnd - snpEnd) + exonFrame) % 3) : (((snpStart - exonStart) + exonFrame) % 3); refCodon[0] = getSnpTxBase(gene, exonIx, snpStart, -snpCodonPos); refCodon[1] = getSnpTxBase(gene, exonIx, snpStart, 1 - snpCodonPos); refCodon[2] = getSnpTxBase(gene, exonIx, snpStart, 2 - snpCodonPos); refCodon[3] = '\0'; if (geneIsRc) { reverseComplement(refCodon, strlen(refCodon)); snpCodonPos = 2 - snpCodonPos; } if (pSnpCodonPos != NULL) *pSnpCodonPos = snpCodonPos; if (pRefAA != NULL) { *pRefAA = lookupCodon(refCodon); if (*pRefAA == '\0') *pRefAA = '*'; } } static char *highlightCodonBase(char *codon, int offset) /* If codon is a triplet and offset is 0 to 2, highlight the base at the offset. * Otherwise just return the given codon sequence unmodified. * Don't free the return value! */ { static struct dyString *dy = NULL; if (dy == NULL) dy = dyStringNew(0); dyStringClear(dy); if (strlen(codon) != 3) dyStringAppend(dy, codon); else if (offset == 0) dyStringPrintf(dy, "<B>%c</B>%c%c", codon[0], codon[1], codon[2]); else if (offset == 1) dyStringPrintf(dy, "%c<B>%c</B>%c", codon[0], codon[1], codon[2]); else if (offset == 2) dyStringPrintf(dy, "%c%c<B>%c</B>", codon[0], codon[1], codon[2]); else dyStringAppend(dy, codon); return dy->string; } void printSnp125FunctionInCDS(struct snp125 *snp, char *geneTable, char *geneTrack, struct genePred *gene, int exonIx, char *geneName) /* Show the effect of each observed allele of snp on the given exon of gene. */ { char *refAllele = cloneString(snp->refUCSC); boolean refIsAlpha = isalpha(refAllele[0]); boolean geneIsRc = sameString(gene->strand, "-"), snpIsRc = sameString(snp->strand, "-"); if (geneIsRc && refIsAlpha) reverseComplement(refAllele, strlen(refAllele)); int refAlleleSize = sameString(refAllele, "-") ? 0 : refIsAlpha ? strlen(refAllele) : -1; boolean refIsSingleBase = (refAlleleSize == 1 && refIsAlpha); int snpCodonPos = 0; char refCodon[4], refAA = '\0'; if (refIsSingleBase) getSnp125RefCodonAndSnpPos(snp, gene, exonIx, &snpCodonPos, refCodon, &refAA); char *alleleStr = cloneString(snp->observed); char *indivAlleles[64]; int alleleCount = chopString(alleleStr, "/", indivAlleles, ArraySize(indivAlleles)); int j; for (j = 0; j < alleleCount; j++) { char *al = indivAlleles[j]; boolean alIsAlpha = (isalpha(al[0]) && !sameString(al, "lengthTooLong")); if ((snpIsRc ^ geneIsRc) && alIsAlpha) reverseComplement(al, strlen(al)); char alBase = al[0]; if (alBase == '\0' || sameString(al, refAllele)) continue; int alSize = sameString(al, "-") ? 0 : alIsAlpha ? strlen(al) : -1; if (alSize != refAlleleSize && alSize >= 0 && refAlleleSize >=0) { int diff = alSize - refAlleleSize; if ((diff % 3) != 0) printf(firstTwoColumnsPctS "%s\n", geneTrack, geneName, snpMisoLinkFromFunc("frameshift")); else if (diff > 0) printf(firstTwoColumnsPctS "%s (insertion of %d codon%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("inframe_insertion"), (int)(diff/3), (diff > 3) ? "s" : ""); else printf(firstTwoColumnsPctS "%s (deletion of %d codon%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("inframe_deletion"), (int)(-diff/3), (diff < -3) ? "s" : ""); } else if (alSize == 1 && refIsSingleBase) { char snpCodon[4]; safecpy(snpCodon, sizeof(snpCodon), refCodon); snpCodon[snpCodonPos] = alBase; char snpAA = lookupCodon(snpCodon); if (snpAA == '\0') snpAA = '*'; char refCodonHtml[16], snpCodonHtml[16]; safecpy(refCodonHtml, sizeof(refCodonHtml), highlightCodonBase(refCodon, snpCodonPos)); safecpy(snpCodonHtml, sizeof(snpCodonHtml), highlightCodonBase(snpCodon, snpCodonPos)); if (refAA != snpAA) { if (refAA == '*') printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("stop-loss"), refAA, refCodonHtml, snpAA, snpCodonHtml); else if (snpAA == '*') printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("nonsense"), refAA, refCodonHtml, snpAA, snpCodonHtml); else printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("missense"), refAA, refCodonHtml, snpAA, snpCodonHtml); } else { if (refAA == '*') printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("stop_retained_variant"), refAA, refCodonHtml, snpAA, snpCodonHtml); else printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("coding-synon"), refAA, refCodonHtml, snpAA, snpCodonHtml); } } else printf(firstTwoColumnsPctS "%s %s --> %s\n", geneTrack, geneName, snpMisoLinkFromFunc("cds-synonymy-unknown"), abbreviateAllele(refAllele), abbreviateAllele(al)); } } void printSnp125FunctionInGene(struct snp125 *snp, char *geneTable, char *geneTrack, struct genePred *gene) /* Given a SNP and a gene that overlaps it, say where in the gene it overlaps * and if in CDS, say what effect the coding alleles have. */ { int snpStart = snp->chromStart, snpEnd = snp->chromEnd; int cdsStart = gene->cdsStart, cdsEnd = gene->cdsEnd; boolean geneIsRc = sameString(gene->strand, "-"); char *geneName = getSymbolForGeneName(geneTable, gene->name); int i, iStart = 0, iEnd = gene->exonCount, iIncr = 1; if (geneIsRc) { iStart = gene->exonCount - 1; iEnd = -1; iIncr = -1; } for (i = iStart; i != iEnd; i += iIncr) { int exonStart = gene->exonStarts[i], exonEnd = gene->exonEnds[i]; if (snpEnd > exonStart && snpStart < exonEnd) { if (snpEnd > cdsStart && snpStart < cdsEnd) printSnp125FunctionInCDS(snp, geneTable, geneTrack, gene, i, geneName); else if (cdsEnd > cdsStart) { boolean is5Prime = ((geneIsRc && (snpStart >= cdsEnd)) || (!geneIsRc && (snpEnd < cdsStart))); printf(firstTwoColumnsPctS "%s\n", geneTrack, geneName, snpMisoLinkFromFunc((is5Prime) ? "untranslated-5" : "untranslated-3")); } else printf(firstTwoColumnsPctS "%s\n", geneTrack, geneName, snpMisoLinkFromFunc("ncRNA")); } // SO term splice_region_variant applies to first/last 3 bases of exon // and first/last 3-8 bases of intron if ((i > 0 && snpStart < exonStart+3 && snpEnd > exonStart) || (i < gene->exonCount-1 && snpStart < exonEnd && snpEnd > exonEnd-3)) printf(", %s", snpMisoLinkFromFunc("splice_region_variant")); puts("</TD></TR>"); if (i > 0) { int intronStart = gene->exonEnds[i-1], intronEnd = gene->exonStarts[i]; if (snpEnd < intronStart || snpStart > intronEnd) continue; if (snpStart < intronStart+2 && snpEnd > intronStart) printf(firstTwoColumnsPctS "%s</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc(geneIsRc ? "splice-3" : "splice-5")); else if (snpStart < intronStart+8 && snpEnd > intronStart+2) printf(firstTwoColumnsPctS "%s, %s</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc("intron_variant"), snpMisoLinkFromFunc("splice_region_variant")); else if (snpStart < intronEnd-8 && snpEnd > intronStart+8) printf(firstTwoColumnsPctS "%s</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc("intron")); else if (snpStart < intronEnd-2 && snpEnd > intronEnd-8) printf(firstTwoColumnsPctS "%s, %s</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc("intron_variant"), snpMisoLinkFromFunc("splice_region_variant")); else if (snpStart < intronEnd && snpEnd > intronEnd-2) printf(firstTwoColumnsPctS "%s</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc(geneIsRc ? "splice-5" : "splice-3")); } } } void printSnp125NearGenes(struct sqlConnection *conn, struct snp125 *snp, char *geneTable, char *geneTrack) /* Search upstream and downstream of snp for neigh */ { struct sqlResult *sr; char query[512]; char **row; int snpStart = snp->chromStart, snpEnd = snp->chromEnd; int nearCount = 0; int maxDistance = 10000; /* query to the left: */ sqlSafef(query, sizeof(query), "select name,txEnd,strand from %s " "where chrom = '%s' and txStart < %d and txEnd > %d", geneTable, snp->chrom, snpStart, snpStart - maxDistance); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *gene = row[0]; char *geneName = getSymbolForGeneName(geneTable, gene); int end = sqlUnsigned(row[1]); char *strand = row[2]; boolean isRc = strand[0] == '-'; printf(firstTwoColumnsPctS "%s (%d bases %sstream)</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc(isRc ? "near-gene-5" : "near-gene-3"), (snpStart - end + 1), (isRc ? "up" : "down")); nearCount++; } sqlFreeResult(&sr); /* query to the right: */ sqlSafef(query, sizeof(query), "select name,txStart,strand from %s " "where chrom = '%s' and txStart < %d and txEnd > %d", geneTable, snp->chrom, snpEnd + maxDistance, snpEnd); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *gene = row[0]; char *geneName = getSymbolForGeneName(geneTable, gene); int start = sqlUnsigned(row[1]); char *strand = row[2]; boolean isRc = strand[0] == '-'; printf(firstTwoColumnsPctS "%s (%d bases %sstream)</TD></TR>\n", geneTrack, geneName, snpMisoLinkFromFunc(isRc ? "near-gene-3" : "near-gene-5"), (start - snpEnd + 1), (isRc ? "down" : "up")); nearCount++; } sqlFreeResult(&sr); if (nearCount == 0) printf("<TR><TD>%s </TD><TD></TD><TD>%s</TD></TR>", geneTrack, snpMisoLinkFromFunc("intergenic_variant")); } static struct genePred *getGPsWithFrames(struct sqlConnection *conn, char *geneTable, char *chrom, int start, int end) /* Given a known-to-exist genePred table name and a range, return * genePreds in range with exonFrames populated. */ { struct genePred *gpList = NULL; boolean hasBin; struct sqlResult *sr = hRangeQuery(conn, geneTable, chrom, start, end, NULL, &hasBin); struct sqlConnection *conn2 = hAllocConn(database); boolean hasFrames = (sqlFieldIndex(conn2, geneTable, "exonFrames") == hasBin + 14); char **row; while ((row = sqlNextRow(sr)) != NULL) { int fieldCount = hasBin + (hasFrames ? 15 : 10); struct genePred *gp; if (hasFrames) { gp = genePredExtLoad(row+hasBin, fieldCount); // Some tables have an exonFrames column but it's empty... if (gp->exonFrames == NULL) genePredAddExonFrames(gp); } else { gp = genePredLoad(row+hasBin); genePredAddExonFrames(gp); } slAddHead(&gpList, gp); } sqlFreeResult(&sr); hFreeConn(&conn2); return gpList; } void printSnp125Function(struct trackDb *tdb, struct snp125 *snp) /* If the user has selected a gene track for functional annotation, * report how this SNP relates to any nearby genes. */ { char varName[512]; safef(varName, sizeof(varName), "%s_geneTrack", tdb->track); struct slName *geneTracks = cartOptionalSlNameList(cart, varName); if (geneTracks == NULL && !cartListVarExists(cart, varName)) { char *defaultGeneTracks = trackDbSetting(tdb, "defaultGeneTracks"); if (isNotEmpty(defaultGeneTracks)) geneTracks = slNameListFromComma(defaultGeneTracks); else return; } struct sqlConnection *conn = hAllocConn(database); struct slName *gt; boolean first = TRUE; for (gt = geneTracks; gt != NULL; gt = gt->next) if (sqlTableExists(conn, gt->name)) { if (first) { printf("<BR><B>UCSC's predicted function relative to selected gene tracks:</B>\n"); printf("<TABLE border=0 cellspacing=0 cellpadding=0>\n"); } struct genePred *geneList = getGPsWithFrames(conn, gt->name, snp->chrom, snp->chromStart, snp->chromEnd); struct genePred *gene; char query[256]; char buf[256]; sqlSafef(query, sizeof(query), "select shortLabel from trackDb where tableName='%s'", gt->name); char *shortLabel = sqlQuickQuery(conn, query, buf, sizeof(buf)-1); if (shortLabel == NULL) shortLabel = gt->name; for (gene = geneList; gene != NULL; gene = gene->next) printSnp125FunctionInGene(snp, gt->name, shortLabel, gene); if (geneList == NULL) printSnp125NearGenes(conn, snp, gt->name, shortLabel); first = FALSE; } if (! first) printf("</TABLE>\n"); hFreeConn(&conn); } char *dbSnpFuncFromInt(unsigned char funcCode) /* Translate an integer function code from NCBI into an abbreviated description. * Do not free return value! */ // Might be a good idea to flesh this out with all codes, libify, and share with // snpNcbiToUcsc instead of partially duplicating. { switch (funcCode) { case 3: return "coding-synon"; case 8: return "cds-reference"; case 41: return "nonsense"; case 42: return "missense"; case 43: return "stop-loss"; case 44: return "frameshift"; case 45: return "cds-indel"; default: { static char buf[16]; safef(buf, sizeof(buf), "%d", funcCode); return buf; } } } void printSnp125CodingAnnotations(struct trackDb *tdb, struct snp125 *snp) /* If tdb specifies extra table(s) that contain protein-coding annotations, * show the effects of SNP on transcript coding sequences. */ { char *tables = trackDbSetting(tdb, "codingAnnotations"); if (isEmpty(tables)) return; struct sqlConnection *conn = hAllocConn(database); struct slName *tbl, *tableList = slNameListFromString(tables, ','); struct dyString *query = dyStringNew(0); for (tbl = tableList; tbl != NULL; tbl = tbl->next) { if (!sqlTableExists(conn, tbl->name)) continue; char setting[512]; safef(setting, sizeof(setting), "codingAnnoLabel_%s", tbl->name); char *label = trackDbSettingOrDefault(tdb, setting, NULL); if (label == NULL && endsWith(tbl->name, "DbSnp")) label = "dbSNP"; else label = tbl->name; boolean hasBin = hIsBinned(database, tbl->name); boolean hasCoords = (sqlFieldIndex(conn, tbl->name, "chrom") != -1); int rowOffset = hasBin + (hasCoords ? 3 : 0); dyStringClear(query); sqlDyStringPrintf(query, "select * from %s where name = '%s'", tbl->name, snp->name); if (hasCoords) sqlDyStringPrintf(query, " and chrom = '%s' and chromStart = %d", seqName, snp->chromStart); struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; boolean first = TRUE; while ((row = sqlNextRow(sr)) != NULL) { if (first) { printf("<BR><B>Coding annotations by %s:</B><BR>\n", label); first = FALSE; } struct snp125CodingCoordless *anno = snp125CodingCoordlessLoad(row+rowOffset); int i; boolean gotRef = (anno->funcCodes[0] == 8); for (i = 0; i < anno->alleleCount; i++) { memSwapChar(anno->peptides[i], strlen(anno->peptides[i]), 'X', '*'); if (anno->funcCodes[i] == 8) continue; char *txName = anno->transcript; if (startsWith("NM_", anno->transcript)) txName = getSymbolForGeneName("refGene", anno->transcript); char *func = dbSnpFuncFromInt(anno->funcCodes[i]); printf("%s: %s ", txName, snpMisoLinkFromFunc(func)); if (sameString(func, "frameshift") || sameString(func, "cds-indel")) { puts("<BR>"); continue; } if (gotRef) printf("%s (%s) --> ", anno->peptides[0], highlightCodonBase(anno->codons[0], anno->frame)); printf("%s (%s)<BR>\n", anno->peptides[i], highlightCodonBase(anno->codons[i], anno->frame)); } } sqlFreeResult(&sr); } hFreeConn(&conn); } void printSnp132ExtraColumns(struct trackDb *tdb, struct snp132Ext *snp) /* Print columns new in snp132 */ { // Skip exceptions column; handled below in writeSnpExceptionWithVersion printf("<TR><TD><B><A HREF=\"#Submitters\">Submitter Handles</A> </TD><TD></B>"); int i; for (i=0; i < snp->submitterCount; i++) printf("%s<A HREF=\"https://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?h=%s\" TARGET=_BLANK>" "%s</A>", (i > 0 ? ", " : ""), snp->submitters[i], snp->submitters[i]); printf("</TD></TR>\n"); if (snp->alleleFreqCount > 0) { boolean gotNonIntN = FALSE; double total2NDbl = 0.0; for (i = 0; i < snp->alleleFreqCount; i++) total2NDbl += snp->alleleNs[i]; int total2N = round(total2NDbl); printf("<TR><TD><B><A HREF=\"#AlleleFreq\">Allele Frequencies</A> </B></TD><TD>"); for (i = 0; i < snp->alleleFreqCount; i++) { printf("%s%s: %.3f%% ", (i > 0 ? "; " : ""), snp->alleles[i], (snp->alleleFreqs[i]*100.0)); // alleleNs should be integers (counts of chromosomes in which allele was observed) // but dbSNP extrapolates them from reported frequency and reported sample count, // so sometimes they are not integers. Present them as integers when we can, warn // when we can't. double f = snp->alleleFreqs[i], n = snp->alleleNs[i]; if (f > 0) { int roundedN = round(n); if (fabs(n - roundedN) < 0.01) printf("(%d / %d)", roundedN, total2N); else { gotNonIntN = TRUE; printf("(%.3f / %.3f)", n, total2NDbl); } } } printf("</TR></TABLE>\n"); if (gotNonIntN) printf(" <em>Note: dbSNP extrapolates allele counts from reported frequencies and " "reported 2N sample sizes (total %d); non-integer allele count may imply " "an inaccuracy in one of the reported numbers.</em><BR>\n", total2N); } else puts("</TABLE>"); if (isNotEmpty(snp->bitfields) && differentString(snp->bitfields, "unknown")) { printf("<BR><B><A HREF=\"#Bitfields\">Miscellaneous properties annotated by dbSNP</A>:" "</B>\n\n"); struct slName *bitfields = slNameListFromComma(snp->bitfields); if (slNameInList(bitfields, "clinically-assoc")) printf("<BR> SNP is in OMIM/OMIA and/or " "at least one submitter is a Locus-Specific Database " "("clinically associated")\n"); if (slNameInList(bitfields, "has-omim-omia")) printf("<BR> SNP is in OMIM/OMIA\n"); if (slNameInList(bitfields, "microattr-tpa")) printf("<BR> SNP has a microattribution or third-party annotation\n"); if (slNameInList(bitfields, "submitted-by-lsdb")) printf("<BR> SNP was submitted by Locus-Specific Database\n"); if (slNameInList(bitfields, "maf-5-all-pops")) printf("<BR> Minor Allele Frequency is at least 5%% in all " "populations assayed\n"); else if (slNameInList(bitfields, "maf-5-some-pop")) printf("<BR> Minor Allele Frequency is at least 5%% in at least one " "population assayed\n"); if (slNameInList(bitfields, "genotype-conflict")) printf("<BR> Quality check: Different genotypes have been submitted " "for the same individual\n"); if (slNameInList(bitfields, "rs-cluster-nonoverlapping-alleles")) printf("<BR> Quality check: The reference SNP cluster contains " "submitted SNPs with non-overlapping alleles\n"); if (slNameInList(bitfields, "observed-mismatch")) printf("<BR> Quality check: The reference sequence allele at the " "mapped position is not present in the SNP allele list\n"); puts("<BR>"); } } // Defined below -- call has since moved up from doSnpWithVersion to printSnp125Info // so exceptions appear before our coding annotations. void writeSnpExceptionWithVersion(struct trackDb *tdb, struct snp132Ext *snp, int version); /* Print out descriptions of exceptions, if any, for this snp. */ void printSnp125Info(struct trackDb *tdb, struct snp132Ext *snp, int version) /* print info on a snp125 */ { struct snp125 *snp125 = (struct snp125 *)snp; printSnpOrthoSummary(tdb, snp->name, snp->observed); if (differentString(snp->strand,"?")) printf("<B>Strand: </B>%s<BR>\n", snp->strand); printf("<B>Observed: </B>%s<BR>\n", snp->observed); printSnpAlleleAndOrthos(tdb, snp125, version); puts("<BR><TABLE border=0 cellspacing=0 cellpadding=0>"); if (version <= 127) printf("<TR><TD><B><A HREF=\"#LocType\">Location Type</A></B></TD><TD>%s</TD></TR>\n", snp->locType); printf("<TR><TD><B><A HREF=\"#Class\">Class</A></B></TD><TD>%s</TD></TR>\n", snp->class); printf("<TR><TD><B><A HREF=\"#Valid\">Validation</A></B></TD><TD>%s</TD></TR>\n", snp->valid); printf("<TR><TD><B><A HREF=\"#Func\">Function</A></B></TD><TD>%s</TD></TR>\n", snpMisoLinkFromFunc(snp->func)); printf("<TR><TD><B><A HREF=\"#MolType\">Molecule Type</A> </B></TD><TD>%s</TD></TR>\n", snp->molType); if (snp->avHet>0) printf("<TR><TD><B><A HREF=\"#AvHet\">Average Heterozygosity</A> </TD>" "<TD></B>%.3f +/- %.3f</TD></TR>\n", snp->avHet, snp->avHetSE); printf("<TR><TD><B><A HREF=\"#Weight\">Weight</A></B></TD><TD>%d</TD></TR>\n", snp->weight); if (version >= 132) printSnp132ExtraColumns(tdb, snp); else printf("</TABLE>\n"); printSnp125CodingAnnotations(tdb, snp125); writeSnpExceptionWithVersion(tdb, snp, version); printSnp125Function(tdb, snp125); } static char *getExcDescTable(struct trackDb *tdb) /* Look up snpExceptionDesc in tdb and provide default if not found. Don't free return value! */ { static char excDescTable[128]; char *excDescTableSetting = trackDbSetting(tdb, "snpExceptionDesc"); if (excDescTableSetting) safecpy(excDescTable, sizeof(excDescTable), excDescTableSetting); else safef(excDescTable, sizeof(excDescTable), "%sExceptionDesc", tdb->table); return excDescTable; } static boolean writeOneSnpException(char *exc, char *desc, boolean alreadyFound) /* Print out the description of exc, unless exc is already displayed elsewhere. */ { // Don't bother reporting MultipleAlignments here -- right after this, // we have a whole section about the other mappings. if (differentString(exc, "MultipleAlignments") && // Also exclude a couple that are from dbSNP not UCSC, and noted above (bitfields). differentString(exc, "GenotypeConflict") && differentString(exc, "ClusterNonOverlappingAlleles")) { if (isEmpty(desc)) desc = exc; if (!alreadyFound) printf("<BR><B>UCSC Annotations:</B><BR>\n"); printf("%s<BR>\n", desc); return TRUE; } return FALSE; } void writeSnpExceptionFromTable(struct trackDb *tdb, char *itemName) /* Print out exceptions, if any, for this snp. */ { char *exceptionsTableSetting = trackDbSetting(tdb, "snpExceptions"); char exceptionsTable[128]; if (exceptionsTableSetting) safecpy(exceptionsTable, sizeof(exceptionsTable), exceptionsTableSetting); else safef(exceptionsTable, sizeof(exceptionsTable), "%sExceptions", tdb->table); char *excDescTable = getExcDescTable(tdb); if (hTableExists(database, exceptionsTable) && hTableExists(database, excDescTable)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[1024]; int start = cartInt(cart, "o"); sqlSafef(query, sizeof(query), "select description, %s.exception from %s, %s " "where chrom = \"%s\" and chromStart = %d and name = \"%s\" " "and %s.exception = %s.exception", excDescTable, excDescTable, exceptionsTable, seqName, start, itemName, excDescTable, exceptionsTable); sr = sqlGetResult(conn, query); boolean gotExc = FALSE; while ((row = sqlNextRow(sr))!=NULL) gotExc |= writeOneSnpException(row[1], row[0], gotExc); sqlFreeResult(&sr); hFreeConn(&conn); } } static void writeSnpExceptionFromColumn(struct trackDb *tdb, struct snp132Ext *snp) /* Hash the contents of exception description table, and for each exception listed * in snp->exceptions, print out its description. */ { char *excDescTable = getExcDescTable(tdb); if (hTableExists(database, excDescTable)) { static struct hash *excDesc = NULL; if (excDesc == NULL) { excDesc = hashNew(0); struct sqlConnection *conn = hAllocConn(database); char query[512]; sqlSafef(query, sizeof(query), "select exception,description from %s", excDescTable); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr))!=NULL) hashAdd(excDesc, row[0], cloneString(row[1])); sqlFreeResult(&sr); hFreeConn(&conn); } struct slName *excList = slNameListFromComma(snp->exceptions), *exc; boolean gotExc = FALSE; for (exc = excList; exc != NULL; exc = exc->next) { char *desc = hashFindVal(excDesc, exc->name); gotExc |= writeOneSnpException(exc->name, desc, gotExc); } } } void writeSnpExceptionWithVersion(struct trackDb *tdb, struct snp132Ext *snp, int version) /* Print out descriptions of exceptions, if any, for this snp. */ { if (version >= 132) writeSnpExceptionFromColumn(tdb, snp); else writeSnpExceptionFromTable(tdb, snp->name); } struct snp *snp125ToSnp(struct snp125 *snp125) /* Copy over the bed6 plus observed fields. */ { struct snp *snp; AllocVar(snp); snp->chrom = cloneString(snp125->chrom); snp->chromStart = snp125->chromStart; snp->chromEnd = snp125->chromEnd; snp->name = cloneString(snp125->name); snp->score = snp125->score; if (sameString(snp125->strand, "+")) snp->strand[0] = '+'; else if (sameString(snp125->strand, "-")) snp->strand[0] = '-'; else snp->strand[0] = '?'; snp->strand[1] = '\0'; snp->observed = cloneString(snp125->observed); return snp; } void checkForHgdpGeo(struct sqlConnection *conn, struct trackDb *tdb, char *itemName, int start) { char *hgdpGeoTable = "hgdpGeo"; // make this a trackDb setting if (!hTableExists(database, hgdpGeoTable)) return; struct sqlResult *sr; char **row; char query[512]; sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", hgdpGeoTable, itemName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct hgdpGeo geo; hgdpGeoStaticLoad(row+1, &geo); char title[1024]; safef(title, sizeof(title), "Human Genome Diversity Project SNP" "<IMG name=\"hgdpImgIcon\" height=40 width=55 class='bigBlue' src=\"%s\">", hgdpPngFilePath(itemName)); jsBeginCollapsibleSection(cart, tdb->track, "hgdpGeo", title, FALSE); printf("Note: These annotations are taken directly from the " "<A HREF=\"http://hgdp.uchicago.edu/\" TARGET=_BLANK>HGDP Selection Browser</A>, " "and may indicate the allele on the opposite strand from that given above.<BR>\n"); printf("<B>Ancestral Allele:</B> %c<BR>\n", geo.ancestralAllele); printf("<B>Derived Allele:</B> %c<BR>\n", geo.derivedAllele); printf("<TABLE><TR><TD>\n"); hgdpGeoFreqTable(&geo); printf("</TD><TD valign=top>\n"); hgdpGeoImg(&geo); printf("</TD></TR></TABLE>\n"); jsEndCollapsibleSection(); } sqlFreeResult(&sr); } void checkForHapmap(struct sqlConnection *conn, struct trackDb *tdb, char *itemName) { boolean isPhaseIII = sameString(trackDbSettingOrDefault(tdb, "hapmapPhase", "II"), "III"); boolean gotHapMap = FALSE; char query[512]; if (!isPhaseIII && sqlTableExists(conn, "hapmapAllelesSummary")) { sqlSafef(query, sizeof(query), "select count(*) from hapmapAllelesSummary where name = '%s'", itemName); if (sqlQuickNum(conn, query) > 0) gotHapMap = TRUE; } else { int i; for (i = 0; hapmapPhaseIIIPops[i] != NULL; i++) { char table[HDB_MAX_TABLE_STRING]; safef(table, sizeof(table), "hapmapSnps%s", hapmapPhaseIIIPops[i]); if (sqlTableExists(conn, table)) { sqlSafef(query, sizeof(query), "select count(*) from %s where name = '%s'", table, itemName); if (sqlQuickNum(conn, query) > 0) { gotHapMap = TRUE; break; } } } } struct trackDb *hsTdb = hashFindVal(trackHash, "hapmapSnps"); if (gotHapMap && hsTdb != NULL) { printf("<TR><TD colspan=2><B><A HREF=\"%s", hgTracksPathAndSettings()); // If hapmapSnps is hidden, make it dense; if it's pack etc., leave it alone. if (sameString("hide", cartUsualString(cart, "hapmapSnps", trackDbSettingOrDefault(hsTdb, "visibility", "hide")))) printf("&hapmapSnps=dense"); printf("\"> HapMap SNP</A> </B></TD></TR>\n"); } } static void checkForGwasCatalog(struct sqlConnection *conn, struct trackDb *tdb, char *item) /* If item is in gwasCatalog, add link to make the track visible. */ { char *gcTable = "gwasCatalog"; if (sqlTableExists(conn, gcTable)) { char query[512]; sqlSafef(query, sizeof(query), "select count(*) from %s where name = '%s'", gcTable, item); if (sqlQuickNum(conn, query) > 0) { struct trackDb *gcTdb = hashFindVal(trackHash, gcTable); if (gcTdb != NULL) { printf("<TR><TD colspan=2>><B><A HREF=\"%s", hgTracksPathAndSettings()); // If gcTable is hidden, make it dense; otherwise, leave it alone. if (sameString("hide", cartUsualString(cart, gcTable, trackDbSettingOrDefault(gcTdb, "visibility", "hide")))) printf("&%s=dense", gcTable); printf("\">%s SNP</A> </B></TD></TR>\n", gcTdb->shortLabel); } } } } static void checkForMupit(struct sqlConnection *conn, struct trackDb *tdb, int start) /* Print a link to MuPIT if the item is in the mupitRanges table */ { if (sqlTableExists(conn, "mupitRanges")) { struct sqlResult *sr = hRangeQuery(conn, "mupitRanges", seqName, start, start+1, NULL, NULL); char **row = NULL; if ((row = sqlNextRow(sr)) != NULL) { int mupitPosition = start + 1; // mupit uses 1-based coords printf("<TR><TD colspan=2><B>"); if (sameString(database, "hg19")) printf("<A HREF=\"http://hg19.cravat.us/MuPIT_Interactive/?gm=%s:%d\">", seqName, mupitPosition); else if (sameString(database, "hg38")) printf("<A HREF=\"http://mupit.icm.jhu.edu/MuPIT_Interactive/?gm=%s:%d\">", seqName, mupitPosition); printf("MuPIT Structure</A></B></TD></TR>\n"); } } } void printOtherSnpMappings(char *table, char *name, int start, struct sqlConnection *conn, int rowOffset) /* If this SNP (from any bed4+ table) is not uniquely mapped, print the other mappings. */ { char query[512]; sqlSafef(query, sizeof(query), "select * from %s where name='%s'", table, name); struct sqlResult *sr = sqlGetResult(conn, query); int snpCount = 0; char **row; while ((row = sqlNextRow(sr)) != NULL) { struct bed *snp = bedLoad3(row + rowOffset); if (snp->chromStart != start || differentString(snp->chrom, seqName)) { printf("<BR>\n"); if (snpCount == 0) printf("<B>This SNP maps to these additional locations:</B><BR><BR>\n"); snpCount++; bedPrintPos((struct bed *)snp, 3, tdb); } } sqlFreeResult(&sr); } void doSnpWithVersion(struct trackDb *tdb, char *itemName, int version) /* Process SNP details. */ { char *table = tdb->table; struct snp132Ext *snp; struct snp *snpAlign = NULL; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[512]; int rowOffset=hOffsetPastBin(database, seqName, table); genericHeader(tdb, NULL); printf("<H2>dbSNP build %d %s</H2>\n", version, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom='%s' and " "chromStart=%d and name='%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if (version >= 132) snp = snp132ExtLoad(row+rowOffset); else snp = (struct snp132Ext *)snp125Load(row+rowOffset); printCustomUrl(tdb, itemName, FALSE); bedPrintPos((struct bed *)snp, 3, tdb); snpAlign = snp125ToSnp((struct snp125 *)snp); printf("<BR>\n"); printSnp125Info(tdb, snp, version); doSnpEntrezGeneLink(tdb, itemName); } else errAbort("SNP %s not found at %s base %d", itemName, seqName, start); sqlFreeResult(&sr); printOtherSnpMappings(table, itemName, start, conn, rowOffset); puts("<BR>"); // Make table for collapsible sections: puts("<TABLE>"); checkForGwasCatalog(conn, tdb, itemName); checkForHgdpGeo(conn, tdb, itemName, start); checkForHapmap(conn, tdb, itemName); checkForMupit(conn, tdb, start); printSnpAlignment(tdb, snpAlign, version); puts("</TABLE>"); printTrackHtml(tdb); hFreeConn(&conn); } void doTigrGeneIndex(struct trackDb *tdb, char *item) /* Put up info on tigr gene index item. */ { char *animal = cloneString(item); char *id = strchr(animal, '_'); char buf[128]; if (id == NULL) { animal = "human"; id = item; } else *id++ = 0; if (sameString(animal, "cow")) animal = "cattle"; else if (sameString(animal, "chicken")) animal = "g_gallus"; else if (sameString(animal, "Dmelano")) animal = "drosoph"; safef(buf, sizeof buf, "species=%s&tc=%s ", animal, id); genericClickHandler(tdb, item, buf); } void doJaxQTL(struct trackDb *tdb, char *item) /* Put up info on Quantitative Trait Locus from Jackson Lab. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; char **row; int start = cartInt(cart, "o"); boolean isBed4 = startsWith("bed 4", tdb->type); boolean hasBin = hIsBinned(database, tdb->table); genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { char *itemForUrl=NULL, *name=NULL, *description=NULL, *marker=NULL; float cMscore = 0.0; struct bed *bed = bedLoadN(row+hasBin, 4); if (isBed4) { char *oDb = trackDbSetting(tdb, "otherDb"); char *oTable = trackDbSetting(tdb, "otherDbTable"); itemForUrl = name = bed->name; if (isNotEmpty(oDb) && isNotEmpty(oTable)) { struct sqlConnection *conn2 = hAllocConn(database); char buf[1024]; sqlSafef(query, sizeof(query), "select description from %s.%s where name = '%s'", oDb, oTable, name); description = cloneString(sqlQuickQuery(conn2, query, buf, sizeof(buf)-1)); sqlSafef(query, sizeof(query), "select mgiID from %s.%s where name = '%s'", oDb, oTable, name); itemForUrl = cloneString(sqlQuickQuery(conn2, query, buf, sizeof(buf)-1)); } } else { struct jaxQTL *jaxQTL = jaxQTLLoad(row); itemForUrl = jaxQTL->mgiID; name = jaxQTL->name; description = jaxQTL->description; cMscore = jaxQTL->cMscore; marker = jaxQTL->marker; } printCustomUrl(tdb, itemForUrl, FALSE); printf("<B>QTL:</B> %s<BR>\n", name); if (isNotEmpty(description)) printf("<B>Description:</B> %s <BR>\n", description); if (cMscore != 0.0) printf("<B>cM position of marker associated with peak LOD score:</B> " "%3.1f<BR>\n", cMscore); if (isNotEmpty(marker)) printf("<B>MIT SSLP marker with highest correlation:</B> %s<BR>", marker); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } #define GWAS_NOT_REPORTED "<em>Not reported</em>" #define GWAS_NONE_SIGNIFICANT "<em>None significant</em>" static char *subNrNs(char *str) /* The GWAS catalog has "NR" or "NS" for many values -- substitute those with something * more readable. Don't free return value, it might be static. */ { if (isEmpty(str) || sameString("NR", str)) return GWAS_NOT_REPORTED; if (sameString("NS", str)) return GWAS_NONE_SIGNIFICANT; struct dyString *dy1 = dyStringSub(str, "[NR]", "[" GWAS_NOT_REPORTED "]"); struct dyString *dy2 = dyStringSub(dy1->string, "[NS]", "[" GWAS_NONE_SIGNIFICANT "]"); return dyStringCannibalize(&dy2); } static boolean isSnpAndAllele(char *str) /* Return TRUE if str ~ /^rs[0-9]+-.+/ . */ { if (isEmpty(str) || !startsWith("rs", str)) return FALSE; char *p = str + 2; if (! isdigit(*p++)) return FALSE; while (isdigit(*p)) p++; if (*p++ != '-') return FALSE; if (*p == '\0') return FALSE; return TRUE; } static char *splitSnpAndAllele(char *str, char **retAllele) /* If str is a rsID+allele, return the rsID and if retAllele is non-null, set it * to the allele portion. Don't free *retAllele. If str is not rsID+allele, * return NULL. */ { if (isSnpAndAllele(str)) { char *rsID = cloneString(str); char *allele = strchr(rsID, '-'); if (allele == NULL) errAbort("splitSnpAndAllele: isSnpAllele() allowed %s", str); *allele++ = '\0'; if (retAllele != NULL) *retAllele = firstWordInLine(allele); return rsID; } else { if (retAllele != NULL) *retAllele = NULL; return NULL; } } static char *getSnpAlleles(struct sqlConnection *conn, char *snpTable, char *snpName) /* Look up snpName's observed alleles in snpTable. Returns NULL if not found. */ { char query[512]; char buf[256]; // varchar(255) sqlSafef(query, sizeof(query), "select observed from %s where name = '%s'", snpTable, snpName); return cloneString(sqlQuickQuery(conn, query, buf, sizeof(buf)-1)); } static void gwasCatalogCheckSnpAlleles(struct trackDb *tdb, struct gwasCatalog *gc) /* Look up the SNP's observed alleles in the snp track and warn if they are * complementary (hence the risk allele is ambiguous because strand is often * not specified in journal articles). */ { char *snpTable = trackDbSetting(tdb, "snpTable"); if (isEmpty(snpTable)) return; struct sqlConnection *conn = hAllocConn(database); if (sqlTableExists(conn, snpTable) && isSnpAndAllele(gc->riskAllele)) { char *riskAllele = NULL, *strongSNP = splitSnpAndAllele(gc->riskAllele, &riskAllele); char *snpVersion = trackDbSettingOrDefault(tdb, "snpVersion", "?"); char *dbSnpAlleles = getSnpAlleles(conn, snpTable, strongSNP); if (dbSnpAlleles == NULL) dbSnpAlleles = "<em>not found</em>"; boolean showBoth = differentString(strongSNP, gc->name); printf("<B>dbSNP build %s observed alleles for %s%s:</B> %s<BR>\n", snpVersion, (showBoth ? "Strongest SNP " : ""), strongSNP, dbSnpAlleles); if (stringIn("C/G", dbSnpAlleles) || stringIn("A/T", dbSnpAlleles)) printf("<em>Note: when SNP alleles are complementary (A/T or C/G), take care to " "determine the strand/orientation of the given risk allele from the " "original publication (above).</em><BR>\n"); if (showBoth) { dbSnpAlleles = getSnpAlleles(conn, snpTable, gc->name); if (dbSnpAlleles == NULL) dbSnpAlleles = "<em>not found</em>"; printf("<B>dbSNP build %s observed alleles for mapped SNP %s:</B> %s<BR>\n", snpVersion, gc->name, dbSnpAlleles); } } hFreeConn(&conn); } void doGwasCatalog(struct trackDb *tdb, char *item) /* Show details from NHGRI's Genome-Wide Association Study catalog. */ { int itemStart = cartInt(cart, "o"), itemEnd = cartInt(cart, "t"); genericHeader(tdb, item); struct sqlConnection *conn = hAllocConn(database); struct dyString *dy = dyStringNew(512); sqlDyStringPrintf(dy, "select * from %s where chrom = '%s' and ", tdb->table, seqName); hAddBinToQuery(itemStart, itemEnd, dy); sqlDyStringPrintf(dy, "chromStart = %d and name = '%s'", itemStart, item); struct sqlResult *sr = sqlGetResult(conn, dy->string); int rowOffset = hOffsetPastBin(database, seqName, tdb->table); boolean first = TRUE; char **row; while ((row = sqlNextRow(sr)) != NULL) { if (first) first = FALSE; else printf("<HR>\n"); struct gwasCatalog *gc = gwasCatalogLoad(row+rowOffset); printCustomUrl(tdb, item, FALSE); printPos(gc->chrom, gc->chromStart, gc->chromEnd, NULL, TRUE, gc->name); printf("<B>Reported region:</B> %s<BR>\n", gc->region); printf("<B>Publication:</B> %s <em>et al.</em> " "<A HREF=\"", gc->author); printEntrezPubMedUidAbstractUrl(stdout, gc->pubMedID); printf("\" TARGET=_BLANK>%s</A>%s <em>%s.</em> %s<BR>\n", gc->title, (endsWith(gc->title, ".") ? "" : "."), gc->journal, gc->pubDate); printf("<B>Disease or trait:</B> %s<BR>\n", subNrNs(gc->trait)); printf("<B>Initial sample size:</B> %s<BR>\n", subNrNs(gc->initSample)); printf("<B>Replication sample size:</B> %s<BR>\n", subNrNs(gc->replSample)); printf("<B>Reported gene(s):</B> %s<BR>\n", subNrNs(gc->genes)); char *strongAllele = NULL, *strongRsID = splitSnpAndAllele(gc->riskAllele, &strongAllele); if (strongRsID) { printf("<B>Strongest SNP-Risk allele:</B> "); printDbSnpRsUrl(strongRsID, "%s", strongRsID); printf("-%s<BR>\n", strongAllele); } else printf("<B>Strongest SNP-Risk allele:</B> %s<BR>\n", subNrNs(gc->riskAllele)); gwasCatalogCheckSnpAlleles(tdb, gc); printf("<B>Risk Allele Frequency:</B> %s<BR>\n", subNrNs(gc->riskAlFreq)); if (isEmpty(gc->pValueDesc) || sameString(gc->pValueDesc, "NS")) printf("<B>p-Value:</B> %s<BR>\n", subNrNs(gc->pValue)); else if (gc->pValueDesc[0] == '(') printf("<B>p-Value:</B> %s %s<BR>\n", gc->pValue, subNrNs(gc->pValueDesc)); else printf("<B>p-Value:</B> %s (%s)<BR>\n", gc->pValue, subNrNs(gc->pValueDesc)); printf("<B>Odds Ratio or beta:</B> %s<BR>\n", subNrNs(gc->orOrBeta)); printf("<B>95%% confidence interval:</B> %s<BR>\n", subNrNs(gc->ci95)); printf("<B>Platform:</B> %s<BR>\n", subNrNs(gc->platform)); printf("<B>Copy Number Variant (CNV)?:</B> %s<BR>\n", (gc->cnv == gwasCatalogY ? "Yes" : "No")); } sqlFreeResult(&sr); printTrackHtml(tdb); } void ncRnaPrintPos(struct bed *bed, int bedSize) /* Print first two fields of an ncRna entry in * standard format. */ { char *strand = NULL; if (bedSize >= 4) printf("<B>Item:</B> %s<BR>\n", bed->name); if (bedSize >= 6) { strand = bed->strand; } printPos(bed->chrom, bed->chromStart, bed->chromEnd, strand, TRUE, bed->name); } void doNcRna(struct trackDb *tdb, char *item) /* Handle click in ncRna track. */ { struct ncRna *ncRna; char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; struct sqlConnection *conn = hAllocConn(database); int bedSize; genericHeader(tdb, item); bedSize = 8; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", table, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { ncRna = ncRnaLoad(row); printCustomUrl(tdb, item, TRUE); printf("<B>Type:</B> %s<BR>", ncRna->type); if (ncRna->extGeneId != NULL && !sameWord(ncRna->extGeneId, "")) { printf("<B>External Gene ID:</B> %s<BR>", ncRna->extGeneId); } bed = bedLoadN(row+hasBin, bedSize); ncRnaPrintPos(bed, bedSize); } sqlFreeResult(&sr); printTrackHtml(tdb); } void doWgRna(struct trackDb *tdb, char *item) /* Handle click in wgRna track. */ { struct wgRna *wgRna; char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; struct sqlConnection *conn = hAllocConn(database); int bedSize; genericHeader(tdb, item); bedSize = 8; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", table, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { wgRna = wgRnaLoad(row); /* display appropriate RNA type and URL */ if (sameWord(wgRna->type, "HAcaBox")) { printCustomUrl(tdb, item, TRUE); printf("<B>RNA Type:</B> H/ACA Box snoRNA\n"); } if (sameWord(wgRna->type, "CDBox")) { printCustomUrl(tdb, item, TRUE); printf("<B>RNA Type:</B> CD Box snoRNA\n"); } if (sameWord(wgRna->type, "scaRna")) { printCustomUrl(tdb, item, TRUE); printf("<B>RNA Type:</B> small Cajal body-specific RNA\n"); } if (sameWord(wgRna->type, "miRna")) { printOtherCustomUrl(tdb, item, "url2", TRUE); printf("<B>RNA Type:</B> microRNA\n"); } printf("<BR>"); bed = bedLoadN(row+hasBin, bedSize); bedPrintPos(bed, bedSize, tdb); } sqlFreeResult(&sr); printTrackHtml(tdb); } void doJaxQTL3(struct trackDb *tdb, char *item) /* Put up info on Quantitative Trait Locus from Jackson Lab. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; int start = cartInt(cart, "o"); struct jaxQTL3 *jaxQTL; genericHeader(tdb, item); sqlSafef(query, sizeof query, "select * from jaxQTL3 where name = '%s' and chrom = '%s' and chromStart = %d", item, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { jaxQTL = jaxQTL3Load(row); printf("<B>Jax/MGI Link: </B>"); printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/marker/%s\">%s</a><BR>\n", jaxQTL->mgiID, jaxQTL->mgiID); printf("<B>QTL:</B> %s<BR>\n", jaxQTL->name); printf("<B>Description:</B> %s <BR>\n", jaxQTL->description); if (!sameWord("", jaxQTL->flank1)) { printf("<B>Flank Marker 1: </B>"); printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->flank1); printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->flank1); } if (!sameWord("", jaxQTL->marker)) { printf("<B>Peak Marker: </B>"); printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->marker); printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->marker); } if (!sameWord("", jaxQTL->flank2)) { printf("<B>Flank Marker 2: </B>"); printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->flank2); printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->flank2); } /* no cMscore for current release*/ /*printf("<B>cM position of marker associated with peak LOD score:</B> %3.1f<BR>\n", jaxQTL->cMscore); */ printf("<B>Chromosome:</B> %s<BR>\n", skipChr(seqName)); printBand(seqName, start, 0, FALSE); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doJaxAllele(struct trackDb *tdb, char *item) /* Show gene prediction position and other info. */ { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); boolean hasBin; char aliasTable[256], phenoTable[256]; struct sqlResult *sr = NULL; char **row = NULL; boolean first = TRUE; genericHeader(tdb, item); safef(aliasTable, sizeof(aliasTable), "%sInfo", tdb->table); safef(phenoTable, sizeof(phenoTable), "jaxAllelePheno"); sqlSafefFrag(query, sizeof(query), "name = \"%s\"", item); sr = hRangeQuery(conn, tdb->table, seqName, winStart, winEnd, query, &hasBin); while ((row = sqlNextRow(sr)) != NULL) { struct bed *bed = bedLoadN(row+hasBin, 12); /* Watch out for case-insensitive matches (e.g. one allele is <sla>, * another is <Sla>): */ if (! sameString(bed->name, item)) continue; if (first) first = FALSE; else printf("<BR>"); printf("<B>MGI Representative Transcript:</B> "); htmTextOut(stdout, bed->name); puts("<BR>"); if (hTableExists(database, aliasTable)) { struct sqlResult *sr2 = NULL; char **row2 = NULL; char query2[1024]; sqlSafef(query2, sizeof(query2), "select mgiId,source,name from %s where name = '%s'", aliasTable, bed->name); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { /* Watch out for case-insensitive matches: */ if (! sameString(bed->name, row2[2])) continue; if (isNotEmpty(row2[0])) printCustomUrl(tdb, row2[0], TRUE); printf("<B>Allele Type:</B> %s<BR>\n", row2[1]); } sqlFreeResult(&sr2); } if (hTableExists(database, phenoTable)) { struct sqlResult *sr2 = NULL; char **row2 = NULL; char query2[1024]; struct slName *phenoList, *pheno; sqlSafef(query2, sizeof(query2), "select phenotypes,allele from %s where allele = '%s'", phenoTable, bed->name); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { /* Watch out for case-insensitive matches: */ if (! sameString(bed->name, row2[1])) continue; boolean firstP = TRUE; phenoList = slNameListFromComma(row2[0]); slNameSort(&phenoList); printf("<B>Associated Phenotype(s):</B> "); for (pheno = phenoList; pheno != NULL; pheno = pheno->next) { if (firstP) firstP = FALSE; else printf(", "); printf("%s", pheno->name); } printf("<BR>\n"); } sqlFreeResult(&sr2); } printPos(bed->chrom, bed->chromStart, bed->chromEnd, bed->strand, FALSE, NULL); bedFree(&bed); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn2); hFreeConn(&conn); } void doJaxPhenotype(struct trackDb *tdb, char *item) /* Show gene prediction position and other info. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; boolean hasBin; char query[512]; char aliasTable[256], phenoTable[256]; struct slName *phenoList = NULL, *pheno = NULL; boolean first = TRUE; char *selectedPheno = NULL; /* Parse out the selected phenotype passed in from hgTracks. */ if ((selectedPheno = strstr(item, " source=")) != NULL) { *selectedPheno = '\0'; selectedPheno += strlen(" source="); } genericHeader(tdb, item); safef(aliasTable, sizeof(aliasTable), "%sAlias", tdb->table); safef(phenoTable, sizeof(phenoTable), "jaxAllelePheno"); sqlSafefFrag(query, sizeof(query), "name = \"%s\"", item); sr = hRangeQuery(conn, tdb->table, seqName, winStart, winEnd, query, &hasBin); while ((row = sqlNextRow(sr)) != NULL) { struct bed *bed = bedLoadN(row+hasBin, 12); if (first) { first = FALSE; printf("<B>MGI Representative Transcript:</B> "); htmTextOut(stdout, bed->name); puts("<BR>"); if (hTableExists(database, aliasTable)) { struct sqlConnection *conn2 = hAllocConn(database); char query2[512]; char buf[512]; char *mgiId; sqlSafef(query2, sizeof(query2), "select alias from %s where name = '%s'", aliasTable, item); mgiId = sqlQuickQuery(conn2, query2, buf, sizeof(buf)); if (mgiId != NULL) printCustomUrl(tdb, mgiId, TRUE); hFreeConn(&conn2); } printPos(bed->chrom, bed->chromStart, bed->chromEnd, bed->strand, FALSE, NULL); bedFree(&bed); } pheno = slNameNew(row[hasBin+12]); slAddHead(&phenoList, pheno); } sqlFreeResult(&sr); printf("<B>Phenotype(s) at this locus: </B> "); first = TRUE; slNameSort(&phenoList); for (pheno = phenoList; pheno != NULL; pheno = pheno->next) { if (first) first = FALSE; else printf(", "); if (selectedPheno && sameString(pheno->name, selectedPheno)) printf("<B>%s</B>", pheno->name); else printf("%s", pheno->name); } puts("<BR>"); if (hTableExists(database, phenoTable) && selectedPheno) { struct trackDb *alleleTdb = hMaybeTrackInfo(conn, "jaxAllele"); struct sqlConnection *conn2 = hAllocConn(database); char query2[512]; char buf[512]; char alleleTable[256]; safef(alleleTable, sizeof(alleleTable), "jaxAlleleInfo"); boolean gotAllele = hTableExists(database, alleleTable); sqlSafef(query, sizeof(query), "select allele from %s where transcript = '%s' " "and phenotypes like '%%%s%%'", phenoTable, item, selectedPheno); first = TRUE; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *mgiId = NULL; if (first) { first = FALSE; printf("<B>Allele(s) Associated with %s Phenotype:</B> ", selectedPheno); } else printf(", "); if (gotAllele) { sqlSafef(query2, sizeof(query2), "select mgiID from jaxAlleleInfo where name = '%s'", row[0]); mgiId = sqlQuickQuery(conn2, query2, buf, sizeof(buf)); } if (mgiId && alleleTdb && alleleTdb->url) { struct dyString *dy = dyStringSub(alleleTdb->url, "$$", mgiId); printf("<A HREF=\"%s\" TARGET=_BLANK>", dy->string); dyStringFree(&dy); } htmTextOut(stdout, row[0]); if (mgiId && alleleTdb && alleleTdb->url) printf("</A>"); } sqlFreeResult(&sr); hFreeConn(&conn2); if (!first) puts("<BR>"); } printTrackHtml(tdb); hFreeConn(&conn); } void doJaxAliasGenePred(struct trackDb *tdb, char *item) /* Show gene prediction position and other info. */ { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); struct genePred *gpList = NULL, *gp = NULL; boolean hasBin; char table[HDB_MAX_TABLE_STRING]; char aliasTable[256]; boolean gotAlias = FALSE; genericHeader(tdb, item); safef(aliasTable, sizeof(aliasTable), "%sAlias", tdb->table); gotAlias = hTableExists(database, aliasTable); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafefFrag(query, sizeof(query), "name = \"%s\"", item); gpList = genePredReaderLoadQuery(conn, table, query); for (gp = gpList; gp != NULL; gp = gp->next) { if (gotAlias) { char query2[1024]; char buf[512]; char *mgiId; sqlSafef(query2, sizeof(query2), "select alias from %s where name = '%s'", aliasTable, item); mgiId = sqlQuickQuery(conn2, query2, buf, sizeof(buf)); if (mgiId != NULL) printCustomUrl(tdb, mgiId, TRUE); } printPos(gp->chrom, gp->txStart, gp->txEnd, gp->strand, FALSE, NULL); if (gp->next != NULL) printf("<br>"); } printTrackHtml(tdb); genePredFreeList(&gpList); hFreeConn(&conn2); hFreeConn(&conn); } void doEncodeRegion(struct trackDb *tdb, char *item) /* Print region desription, along with generic info */ { char *descr; char *plus = NULL; char buf[128]; if ((descr = getEncodeRegionDescr(item)) != NULL) { safef(buf, sizeof(buf), "<B>Description:</B> %s<BR>\n", descr); plus = buf; } genericClickHandlerPlus(tdb, item, NULL, plus); } char *getEncodeName(char *item) /* the item is in the format 'ddddddd/nnn' where the first seven 'd' characters are the digits of the identifier, and the variable-length 'n' chatacters are the name of the object. Return the name. */ { char *dupe=cloneString(item); return dupe+8; } char *getEncodeId(char *item) /* the item is in the format 'ddddddd/nnn' where the first seven 'd' characters are the digits of the identifier, and the variable-length 'n' chatacters are the name of the object. Return the ID portion. */ { char *id = cloneString(item); id[7]='\0'; return id; } void doEncodeErge(struct trackDb *tdb, char *item) /* Print ENCODE data from dbERGE II */ { struct sqlConnection *conn = hAllocConn(database); char query[1024]; struct encodeErge *ee=NULL; int start = cartInt(cart, "o"); char *newLabel = tdb->longLabel + 7; /* removes 'ENCODE ' from label */ char *encodeName = getEncodeName(item); char *encodeId = getEncodeId(item); cartWebStart(cart, database, "ENCODE Region Data: %s", newLabel); printf("<H2>ENCODE Region <span style='text-decoration:underline;'>%s</span> Data for %s.</H2>\n", newLabel, encodeName); genericHeader(tdb, encodeName); genericBedClick(conn, tdb, item, start, 14); /* reserved field has changed to itemRgb in code 2004-11-22 - Hiram */ sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd, name, score, strand, " " thickStart, thickEnd, reserved, blockCount, blockSizes, " " chromStarts, Id, color " "from %s " "where name = '%s' and chromStart = %d " "order by Id ", tdb->table, item, start); for (ee = encodeErgeLoadByQuery(conn, query); ee!=NULL; ee=ee->next) { printf("<BR>\n"); if (ee->Id>0) { printf("<BR>Additional information for <A HREF=\"http://dberge.cse.psu.edu/"); printf("cgi-bin/dberge_query?mode=Submit+query&disp=brow+data&pid="); printf("%s\" TARGET=_blank>%s</A>\n is available from <A ", encodeId, encodeName); printf("HREF=\"http://globin.cse.psu.edu/dberge/testmenu.html\" "); printf("TARGET=_blank>dbERGEII</A>.\n"); } } printTrackHtml(tdb); encodeErgeFree(&ee); hFreeConn(&conn); } void doEncodeErgeHssCellLines(struct trackDb *tdb, char *item) /* Print ENCODE data from dbERGE II */ { struct sqlConnection *conn = hAllocConn(database); char query[1024]; struct encodeErgeHssCellLines *ee=NULL; int start = cartInt(cart, "o"); char *dupe, *words[16]; int wordCount=0; char *encodeName = getEncodeName(item); char *encodeId = getEncodeId(item); int i; cartWebStart(cart, database, "ENCODE Region Data: %s", tdb->longLabel+7); printf("<H2>ENCODE Region <span style='text-decoration:underline;'>%s</span> Data for %s</H2>\n", tdb->longLabel+7, encodeName); genericHeader(tdb, item); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); genericBedClick(conn, tdb, item, start, atoi(words[1])); /* reserved field has changed to itemRgb in code 2004-11-22 - Hiram */ sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd, name, score, strand, " " thickStart, thickEnd, reserved, blockCount, blockSizes, " " chromStarts, Id, color, allLines " "from %s " "where name = '%s' and chromStart = %d " "order by Id ", tdb->table, item, start); for (ee = encodeErgeHssCellLinesLoadByQuery(conn, query); ee!=NULL; ee=ee->next) { if (ee->Id>0) { printf("<BR><B>Cell lines:</B> "); dupe = cloneString(ee->allLines); wordCount = chopCommas(dupe, words); for (i=0; i<wordCount-1; i++) { printf("%s, ", words[i]); } printf("%s.\n",words[wordCount-1]); printf("<BR><BR>Additional information for <A HREF=\"http://dberge.cse.psu.edu/"); printf("cgi-bin/dberge_query?mode=Submit+query&disp=brow+data&pid="); printf("%s\" TARGET=_blank>%s</A>\n is available from <A ", encodeId, encodeName); printf("HREF=\"http://globin.cse.psu.edu/dberge/testmenu.html\" "); printf("TARGET=_blank>dbERGEII</A>.\n"); } } printTrackHtml(tdb); encodeErgeHssCellLinesFree(&ee); hFreeConn(&conn); } void doEncodeIndels(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct encodeIndels encodeIndel; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); boolean firstTime = TRUE; genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { encodeIndelsStaticLoad(row+rowOffset, &encodeIndel); if (firstTime) { printf("<B>Variant and Reference Sequences: </B><BR>\n"); printf("<PRE><TT>%s<BR>\n", encodeIndel.variant); printf("%s</TT></PRE><BR>\n", encodeIndel.reference); bedPrintPos((struct bed *)&encodeIndel, 3, tdb); firstTime = FALSE; printf("-----------------------------------------------------<BR>\n"); } printf("<B>Trace Name:</B> %s <BR>\n", encodeIndel.traceName); printf("<B>Trace Id:</B> "); printf("<A HREF=\"%s\" TARGET=_blank> %s</A> <BR>\n", traceUrl(encodeIndel.traceId), encodeIndel.traceId); printf("<B>Trace Pos:</B> %d <BR>\n", encodeIndel.tracePos); printf("<B>Trace Strand:</B> %s <BR>\n", encodeIndel.traceStrand); printf("<B>Quality Score:</B> %d <BR>\n", encodeIndel.score); printf("-----------------------------------------------------<BR>\n"); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doGbProtAnn(struct trackDb *tdb, char *item) /* Show extra info for GenBank Protein Annotations track. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; int start = cartInt(cart, "o"); struct gbProtAnn *gbProtAnn; genericHeader(tdb, item); sqlSafef(query, sizeof query, "select * from gbProtAnn where name = '%s' and chrom = '%s' and chromStart = %d", item, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { gbProtAnn = gbProtAnnLoad(row); printCustomUrl(tdb, item, TRUE); printf("<B>Product:</B> %s<BR>\n", gbProtAnn->product); if (gbProtAnn->note[0] != 0) printf("<B>Note:</B> %s <BR>\n", gbProtAnn->note); printf("<B>GenBank Protein: </B>"); printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=%s\"", gbProtAnn->proteinId); printf(" TARGET=_blank>%s</A><BR>\n", gbProtAnn->proteinId); htmlHorizontalLine(); showSAM_T02(gbProtAnn->proteinId); printPos(seqName, gbProtAnn->chromStart, gbProtAnn->chromEnd, "+", TRUE, gbProtAnn->name); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } bool matchTableOrHandler(char *word, struct trackDb *tdb) /* return true if word matches either the table name or the trackHandler setting of the tdb struct */ { if (NULL == tdb) return FALSE; char* handler = trackDbSetting(tdb, "trackHandler"); return (sameWord(word, tdb->table) || (handler!=NULL && sameWord(word, handler))); } void doLinkedFeaturesSeries(char *track, char *clone, struct trackDb *tdb) /* Create detail page for linked features series tracks */ { char query[256]; char title[256]; struct sqlConnection *conn = hAllocConn(database), *conn1 = hAllocConn(database); struct sqlResult *sr = NULL, *sr2 = NULL, *srb = NULL; char **row, **row1, **row2, **rowb; char *lfLabel = NULL; char *table = NULL; char *intName = NULL; char pslTable[HDB_MAX_TABLE_STRING]; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); int length = end - start; int i; struct lfs *lfs; struct psl *pslList = NULL, *psl; boolean hasBin = hOffsetPastBin(database, seqName, track); /* Determine type */ if (matchTableOrHandler("bacEndPairs", tdb)) { safef(title, sizeof title, "Location of %s using BAC end sequences", clone); lfLabel = "BAC ends"; table = track; } if (matchTableOrHandler("bacEndSingles", tdb)) { safef(title, sizeof title, "Location of %s using BAC end sequences", clone); lfLabel = "BAC ends"; table = track; } if (matchTableOrHandler("bacEndPairsBad", tdb)) { safef(title, sizeof title, "Location of %s using BAC end sequences", clone); lfLabel = "BAC ends"; table = track; } if (matchTableOrHandler("bacEndPairsLong", tdb)) { safef(title, sizeof title, "Location of %s using BAC end sequences", clone); lfLabel = "BAC ends"; table = track; } if (matchTableOrHandler("fosEndPairs", tdb)) { safef(title, sizeof title, "Location of %s using fosmid end sequences", clone); lfLabel = "Fosmid ends"; table = track; } if (matchTableOrHandler("fosEndPairsBad", tdb)) { safef(title, sizeof title, "Location of %s using fosmid end sequences", clone); lfLabel = "Fosmid ends"; table = track; } if (matchTableOrHandler("fosEndPairsLong", tdb)) { safef(title, sizeof title, "Location of %s using fosmid end sequences", clone); lfLabel = "Fosmid ends"; table = track; } if (matchTableOrHandler("earlyRep", tdb)) { safef(title, sizeof title, "Location of %s using cosmid end sequences", clone); lfLabel = "Early Replication Cosmid Ends"; table = track; } if (matchTableOrHandler("earlyRepBad", tdb)) { safef(title, sizeof title, "Location of %s using cosmid end sequences", clone); lfLabel = "Early Replication Cosmid Ends"; table = track; } if (trackDbSetting(tdb, "lfPslTable")) { safef(title, sizeof title, "Location of %s using clone end sequences", clone); lfLabel = "Clone ends"; table = track; } /* Print out non-sequence info */ cartWebStart(cart, database, "%s", title); /* Find the instance of the object in the bed table */ sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", table, clone, seqName, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { lfs = lfsLoad(row+hasBin); if (sameString("bacEndPairs", track) || sameString("bacEndSingles", track)) { if (sameString("Zebrafish", organism) ) { /* query to bacCloneXRef table to get Genbank accession */ /* and internal Sanger name for clones */ sqlSafef(query, sizeof query, "SELECT genbank, intName FROM bacCloneXRef WHERE name = '%s'", clone); srb = sqlMustGetResult(conn1, query); rowb = sqlNextRow(srb); if (rowb != NULL) { printf("<H2><A HREF="); printCloneDbUrl(stdout, clone); printf(" TARGET=_BLANK>%s</A></H2>\n", clone); if (rowb[0] != NULL) { printf("<H3>Genbank Accession: <A HREF="); printEntrezNucleotideUrl(stdout, rowb[0]); printf(" TARGET=_BLANK>%s</A></H3>\n", rowb[0]); } else printf("<H3>Genbank Accession: n/a"); intName = cloneString(rowb[1]); } else printf("<H2>%s</H2>\n", clone); } else if (sameString("Dog", organism) || sameString("Zebra finch", organism)) { printf("<H2><A HREF="); printTraceUrl(stdout, "clone_id", clone); printf(" TARGET=_BLANK>%s</A></H2>\n", clone); } else if (trackDbSetting(tdb, "notNCBI")) { printf("<H2>%s</H2>\n", clone); } else if (startsWith(tdb->track, "trace")) { printTraceUrl(stdout, "clone_id", clone); } else { printf("<H2><A HREF="); printCloneDbUrl(stdout, clone); printf(" TARGET=_BLANK>%s</A></H2>\n", clone); } } else if (trackDbSetting(tdb, "lfPslTable")) { printf("<H2><A HREF="); printCloneDbUrl(stdout, clone); printf(" TARGET=_BLANK>%s</A></H2>\n", clone); } else { printf("<B>%s</B>\n", clone); } printf("<P><HR ALIGN=\"CENTER\"></P>\n<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n",seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printf("<TR><TH ALIGN=left>Length:</TH><TD>%d</TD></TR>\n",length); printf("<TR><TH ALIGN=left>Strand:</TH><TD>%s</TD></TR>\n", lfs->strand); printf("<TR><TH ALIGN=left>Score:</TH><TD>%d</TD></TR>\n", lfs->score); if ((sameString("Zebrafish", organism)) && ((sameString("bacEndPairs", track)) || (sameString("bacEndSingles", track))) ) { /* print Sanger FPC name (internal name) */ printf("<TR><TH ALIGN=left>Sanger FPC Name:</TH><TD>"); if (intName != NULL) printf("%s</TD></TR>\n", intName); else printf("n/a</TD></TR>\n"); /* print associated STS information for this BAC clone */ //printBacStsXRef(clone); } else { printBand(seqName, start, end, TRUE); printf("</TABLE>\n"); printf("<P><HR ALIGN=\"CENTER\"></P>\n"); } if (lfs->score == 1000) { printf("<H4>This is the only location found for %s</H4>\n",clone); } else { //printOtherLFS(clone, table, start, end); } safef(title, sizeof title, "Genomic alignments of %s:", lfLabel); webNewSection("%s",title); for (i = 0; i < lfs->lfCount; i++) { sqlFreeResult(&sr); if (!hFindSplitTable(database, seqName, lfs->pslTable, pslTable, sizeof pslTable, &hasBin)) errAbort("track %s not found", lfs->pslTable); if (isEmpty(pslTable) && trackDbSetting(tdb, "lfPslTable")) safecpy(pslTable, sizeof(pslTable), trackDbSetting(tdb, "lfPslTable")); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE qName = '%s'", pslTable, lfs->lfNames[i]); sr = sqlMustGetResult(conn, query); while ((row1 = sqlNextRow(sr)) != NULL) { psl = pslLoad(row1+hasBin); slAddHead(&pslList, psl); } slReverse(&pslList); if ((!sameString("fosEndPairs", track)) && (!sameString("earlyRep", track)) && (!sameString("earlyRepBad", track))) { if (sameWord(organism, "Zebrafish") ) { /* query to bacEndAlias table to get Genbank accession */ sqlSafef(query, sizeof query, "SELECT * FROM bacEndAlias WHERE alias = '%s' ", lfs->lfNames[i]); sr2 = sqlMustGetResult(conn, query); row2 = sqlNextRow(sr2); if (row2 != NULL) { printf("<H3>%s\tAccession: <A HREF=", lfs->lfNames[i]); printEntrezNucleotideUrl(stdout, row2[2]); printf(" TARGET=_BLANK>%s</A></H3>\n", row2[2]); } else { printf("<B>%s</B>\n",lfs->lfNames[i]); } sqlFreeResult(&sr2); } else if (sameString("Dog", organism) || sameString("Zebra finch", organism)) { printf("<H3><A HREF="); printTraceUrl(stdout, "trace_name", lfs->lfNames[i]); printf(" TARGET=_BLANK>%s</A></H3>\n",lfs->lfNames[i]); } else if (trackDbSetting(tdb, "notNCBI")) { printf("<H3>%s</H3>\n", lfs->lfNames[i]); } else if (trackDbSetting(tdb, "lfPslTable")) { printf("<H3><A HREF="); printTraceTiUrl(stdout, lfs->lfNames[i]); printf(" TARGET=_BLANK>%s</A></H3>\n",lfs->lfNames[i]); } else { printf("<H3><A HREF="); printEntrezNucleotideUrl(stdout, lfs->lfNames[i]); printf(" TARGET=_BLANK>%s</A></H3>\n",lfs->lfNames[i]); } } else { printf("<B>%s</B>\n", lfs->lfNames[i]); } printAlignments(pslList, lfs->lfStarts[i], "htcCdnaAli", lfs->pslTable, lfs->lfNames[i]); htmlHorizontalLine(); pslFreeList(&pslList); } } else { warn("Couldn't find %s in %s table", clone, table); } sqlFreeResult(&sr); sqlFreeResult(&sr2); sqlFreeResult(&srb); webNewSection("Notes:"); printTrackHtml(tdb); hFreeConn(&conn); hFreeConn(&conn1); } void fillCghTable(int type, char *tissue, boolean bold) /* Get the requested records from the database and print out HTML table */ { char query[256]; char currName[64]; int rowOffset; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; struct cgh *cghRow; if (tissue) sqlSafef(query, sizeof query, "type = %d AND tissue = '%s' ORDER BY name, chromStart", type, tissue); else sqlSafef(query, sizeof query, "type = %d ORDER BY name, chromStart", type); sr = hRangeQuery(conn, "cgh", seqName, winStart, winEnd, query, &rowOffset); while ((row = sqlNextRow(sr))) { cghRow = cghLoad(row); if (strcmp(currName,cghRow->name)) { if (bold) printf("</TR>\n<TR>\n<TH>%s</TH>\n",cghRow->name); else printf("</TR>\n<TR>\n<TD>%s</TD>\n",cghRow->name); strcpy(currName,cghRow->name); } if (bold) printf("<TH ALIGN=right>%.6f</TH>\n",cghRow->score); else printf("<TD ALIGN=right>%.6f</TD>\n",cghRow->score); } sqlFreeResult(&sr); } /* Evan Eichler's stuff */ void doCeleraDupPositive(struct trackDb *tdb, char *dupName) /* Handle click on celeraDupPositive track. */ { struct celeraDupPositive dup; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int celeraVersion = 0; int i = 0; cartWebStart(cart, database, "%s", tdb->longLabel); if (sameString(database, "hg15")) celeraVersion = 3; else celeraVersion = 4; if (cgiVarExists("o")) { int start = cgiInt("o"); int rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and name= '%s'", tdb->table, seqName, start, dupName); sr = sqlGetResult(conn, query); i = 0; while ((row = sqlNextRow(sr))) { if (i > 0) htmlHorizontalLine(); celeraDupPositiveStaticLoad(row+rowOffset, &dup); printf("<B>Duplication Name:</B> %s<BR>\n", dup.name); bedPrintPos((struct bed *)(&dup), 3, tdb); if (!sameString(dup.name, dup.fullName)) printf("<B>Full Descriptive Name:</B> %s<BR>\n", dup.fullName); if (dup.bpAlign > 0) { printf("<B>Fraction BP Match:</B> %3.4f<BR>\n", dup.fracMatch); printf("<B>Alignment Length:</B> %3.0f<BR>\n", dup.bpAlign); } if (!startsWith("WSSD No.", dup.name)) { printf("<A HREF=\"http://humanparalogy.gs.washington.edu" "/eichler/celera%d/cgi-bin/celera%d.pl" "?search=%s&type=pdf \" Target=%s_PDF>" "<B>Clone Read Depth Graph (PDF)</B></A><BR>", celeraVersion, celeraVersion, dup.name, dup.name); printf("<A HREF=\"http://humanparalogy.gs.washington.edu" "/eichler/celera%d/cgi-bin/celera%d.pl" "?search=%s&type=jpg \" Target=%s_JPG>" "<B>Clone Read Depth Graph (JPG)</B></A><BR>", celeraVersion, celeraVersion, dup.name, dup.name); } i++; } } else { puts("<P>Click directly on a duplication for information on that " "duplication.</P>"); } printTrackHtml(tdb); hFreeConn(&conn); } void parseSuperDupsChromPointPos(char *pos, char *retChrom, int *retPos, int *retID) /* Parse out (No.)?NNNN[.,]chrN:123 into NNNN and chrN and 123. */ { char *words[16]; int wordCount = 0; char *sep = ",.:"; char *origPos = pos; if (startsWith("No.", pos)) pos += strlen("No."); pos = cloneString(pos); wordCount = chopString(pos, sep, words, ArraySize(words)); if (wordCount < 2 || wordCount > 3) errAbort("parseSuperDupsChromPointPos: Expected something like " "(No\\.)?([0-9]+[.,])?[a-zA-Z0-9_]+:[0-9]+ but got %s", origPos); if (wordCount == 3) { *retID = sqlUnsigned(words[0]); safecpy(retChrom, 64, words[1]); *retPos = sqlUnsigned(words[2]); } else { *retID = -1; safecpy(retChrom, 64, words[0]); *retPos = sqlUnsigned(words[1]); } } void doGenomicSuperDups(struct trackDb *tdb, char *dupName) /* Handle click on genomic dup track. */ { cartWebStart(cart, database, "%s", tdb->longLabel); if (cgiVarExists("o")) { struct genomicSuperDups dup; struct dyString *query = newDyString(512); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char oChrom[64]; int oStart; int dupId; int rowOffset; int start = cgiInt("o"); int end = cgiInt("t"); char *alignUrl = NULL; if (sameString("hg18", database)) alignUrl = "http://humanparalogy.gs.washington.edu/build36"; else if (sameString("hg17", database)) alignUrl = "http://humanparalogy.gs.washington.edu"; else if (sameString("hg15", database) || sameString("hg16", database)) alignUrl = "http://humanparalogy.gs.washington.edu/jab/der_oo33"; rowOffset = hOffsetPastBin(database, seqName, tdb->table); parseSuperDupsChromPointPos(dupName, oChrom, &oStart, &dupId); sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ", tdb->table, seqName); if (rowOffset > 0) hAddBinToQuery(start, end, query); if (dupId >= 0) dyStringPrintf(query, "uid = %d and ", dupId); dyStringPrintf(query, "chromStart = %d and otherStart = %d", start, oStart); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr))) { genomicSuperDupsStaticLoad(row+rowOffset, &dup); bedPrintPos((struct bed *)(&dup), 4, tdb); printf("<B>Other Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">" "%s:%d-%d</A> \n", hgTracksPathAndSettings(), database, dup.otherChrom, dup.otherStart+1, dup.otherEnd, dup.otherChrom, dup.otherStart+1, dup.otherEnd); printf("<A HREF=\"%s&o=%d&t=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&strand=%s&db=%s&table=%s\">" "View DNA for other position</A><BR>\n", hgcPathAndSettings(), dup.otherStart, dup.otherEnd, "", dup.otherChrom, dup.otherStart, dup.otherEnd, dup.strand, database, tdb->track); printf("<B>Other Position Relative Orientation:</B>%s<BR>\n", dup.strand); if(sameString("canFam1", database)) { printf("<B>Filter Verdict:</B> %s<BR>\n", dup.verdict); printf(" <B> testResult:</B>%s<BR>\n", dup.testResult); printf(" <B> chits:</B>%s<BR>\n", dup.chits); printf(" <B> ccov:</B>%s<BR>\n", dup.ccov); printf(" <B> posBasesHit:</B>%d<BR>\n", dup.posBasesHit); } if (alignUrl != NULL) printf("<A HREF=%s/%s " "TARGET=\"%s:%d-%d\">Optimal Global Alignment</A><BR>\n", alignUrl, dup.alignfile, dup.chrom, dup.chromStart, dup.chromEnd); printf("<B>Alignment Length:</B> %d<BR>\n", dup.alignL); printf(" <B>Indels #:</B> %d<BR>\n", dup.indelN); printf(" <B>Indels bp:</B> %d<BR>\n", dup.indelS); printf(" <B>Aligned Bases:</B> %d<BR>\n", dup.alignB); printf(" <B>Matching bases:</B> %d<BR>\n", dup.matchB); printf(" <B>Mismatched bases:</B> %d<BR>\n", dup.mismatchB); printf(" <B>Transitions:</B> %d<BR>\n", dup.transitionsB); printf(" <B>Transverions:</B> %d<BR>\n", dup.transversionsB); printf(" <B>Fraction Matching:</B> %3.4f<BR>\n", dup.fracMatch); printf(" <B>Fraction Matching with Indels:</B> %3.4f<BR>\n", dup.fracMatchIndel); printf(" <B>Jukes Cantor:</B> %3.4f<BR>\n", dup.jcK); } dyStringFree(&query); sqlFreeResult(&sr); hFreeConn(&conn); } else puts("<P>Click directly on a repeat for specific information on that repeat</P>"); printTrackHtml(tdb); } /* end of Evan Eichler's stuff */ void doCgh(char *track, char *tissue, struct trackDb *tdb) /* Create detail page for comparative genomic hybridization track */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; /* Print out non-sequence info */ cartWebStart(cart, database, "%s", tissue); /* Print general range info */ printf("<H2>UCSF Comparative Genomic Hybridizations - %s</H2>\n", tissue); printf("<P><HR ALIGN=\"CENTER\"></P>\n<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n",seqName); printf("<TR><TH ALIGN=left>Start window:</TH><TD>%d</TD></TR>\n",winStart); printf("<TR><TH ALIGN=left>End window:</TH><TD>%d</TD></TR>\n",winEnd); printf("</TABLE>\n"); printf("<P><HR ALIGN=\"CENTER\"></P>\n"); /* Find the names of all of the clones in this range */ printf("<TABLE>\n"); printf("<TR><TH>Cell Line</TH>"); sqlSafef(query, sizeof query, "SELECT spot from cgh where chrom = '%s' AND " "chromStart <= '%d' AND chromEnd >= '%d' AND " "tissue = '%s' AND type = 3 GROUP BY spot ORDER BY chromStart", seqName, winEnd, winStart, tissue); sr = sqlMustGetResult(conn, query); while ((row = sqlNextRow(sr))) printf("<TH>Spot %s</TH>",row[0]); printf("</TR>\n"); sqlFreeResult(&sr); /* Find the relevant tissues type records in the range */ fillCghTable(3, tissue, FALSE); printf("<TR><TD> </TD></TR>\n"); /* Find the relevant tissue average records in the range */ fillCghTable(2, tissue, TRUE); printf("<TR><TD> </TD></TR>\n"); /* Find the all tissue average records in the range */ fillCghTable(1, NULL, TRUE); printf("<TR><TD> </TD></TR>\n"); printf("</TR>\n</TABLE>\n"); hFreeConn(&conn); } void doMcnBreakpoints(char *track, char *name, struct trackDb *tdb) /* Create detail page for MCN breakpoints track */ { char query[256]; char title[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char **row; struct mcnBreakpoints *mcnRecord; /* Print out non-sequence info */ safef(title, sizeof title, "MCN Breakpoints - %s",name); cartWebStart(cart, database, "%s", title); /* Print general range info */ /*printf("<H2>MCN Breakpoints - %s</H2>\n", name); printf("<P><HR ALIGN=\"CENTER\"></P>");*/ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n",seqName); printf("<TR><TH ALIGN=left>Begin in Chromosome:</TH><TD>%d</TD></TR>\n",start); printf("<TR><TH ALIGN=left>End in Chromosome:</TH><TD>%d</TD></TR>\n",end); printBand(seqName, start, end, TRUE); printf("</TABLE>\n"); /* Find all of the breakpoints in this range for this name*/ sqlSafef(query, sizeof query, "SELECT * FROM mcnBreakpoints WHERE chrom = '%s' AND " "chromStart = %d and chromEnd = %d AND name = '%s'", seqName, start, end, name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr))) { printf("<P><HR ALIGN=\"CENTER\"></P>\n"); mcnRecord = mcnBreakpointsLoad(row); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Case ID:</TH><TD>%s</TD></TR>", mcnRecord->caseId); printf("<TR><TH ALIGN=left>Breakpoint ID:</TH><TD>%s</TD></TR>", mcnRecord->bpId); printf("<TR><TH ALIGN=left>Trait:</TH><TD>%s</TD><TD>%s</TD></TR>", mcnRecord->trId, mcnRecord->trTxt); printf("<TR><TH ALIGN=left>Trait Group:</TH><TD>%s</TD><TD>%s</TD></TR>", mcnRecord->tgId, mcnRecord->tgTxt); printf("</TR>\n</TABLE>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); } void doProbeDetails(struct trackDb *tdb, char *item) { struct sqlConnection *conn = hAllocConn(database); struct dnaProbe *dp = NULL; char query[256]; genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select * from dnaProbe where name='%s'", item); dp = dnaProbeLoadByQuery(conn, query); if(dp != NULL) { printf("<h3>Probe details:</h3>\n"); printf("<b>Name:</b> %s <span style='font-size:x-small;'>" "[dbName genomeVersion strand coordinates]</span><br>\n",dp->name); printf("<b>Dna:</b> %s", dp->dna ); printf("[<a href=\"hgBlat?type=DNA&genome=hg8&sort=&query,score&output=hyperlink&userSeq=%s\">blat (blast like alignment)</a>]<br>", dp->dna); printf("<b>Size:</b> %d<br>", dp->size ); printf("<b>Chrom:</b> %s<br>", dp->chrom ); printf("<b>ChromStart:</b> %d<br>", dp->start+1 ); printf("<b>ChromEnd:</b> %d<br>", dp->end ); printf("<b>Strand:</b> %s<br>", dp->strand ); printf("<b>3' Dist:</b> %d<br>", dp->tpDist ); printf("<b>Tm:</b> %f <span style='font-size:x-small;'>" "[scores over 100 are allowed]</span><br>", dp->tm ); printf("<b>%%GC:</b> %f<br>", dp->pGC ); printf("<b>Affy:</b> %d <span style='font-size:x-small;'>" "[1 passes, 0 doesn't pass Affy heuristic]</span><br>", dp->affyHeur ); printf("<b>Sec Struct:</b> %f<br>", dp->secStruct); printf("<b>blatScore:</b> %d<br>", dp->blatScore ); printf("<b>Comparison:</b> %f<br>", dp->comparison); } /* printf("<h3>Genomic Details:</h3>\n"); * genericBedClick(conn, tdb, item, start, 1); */ printTrackHtml(tdb); hFreeConn(&conn); } void doChicken13kDetails(struct trackDb *tdb, char *item) { struct sqlConnection *conn = hAllocConn(database); struct chicken13kInfo *chick = NULL; char query[256]; int start = cartInt(cart, "o"); genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select * from chicken13kInfo where id='%s'", item); chick = chicken13kInfoLoadByQuery(conn, query); if (chick != NULL) { printf("<b>Probe name:</b> %s<br>\n", chick->id); printf("<b>Source:</b> %s<br>\n", chick->source); printf("<b>PCR Amplification code:</b> %s<br>\n", chick->pcr); printf("<b>Library:</b> %s<br>\n", chick->library); printf("<b>Source clone name:</b> %s<br>\n", chick->clone); printf("<b>Library:</b> %s<br>\n", chick->library); printf("<b>Genbank accession:</b> %s<br>\n", chick->gbkAcc); printf("<b>BLAT alignment:</b> %s<br>\n", chick->blat); printf("<b>Source annotation:</b> %s<br>\n", chick->sourceAnnot); printf("<b>TIGR assigned TC:</b> %s<br>\n", chick->tigrTc); printf("<b>TIGR TC annotation:</b> %s<br>\n", chick->tigrTcAnnot); printf("<b>BLAST determined annotation:</b> %s<br>\n", chick->blastAnnot); printf("<b>Comment:</b> %s<br>\n", chick->comment); } genericBedClick(conn, tdb, item, start, 1); printTrackHtml(tdb); hFreeConn(&conn); } void perlegenDetails(struct trackDb *tdb, char *item) { int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; int numSnpsReq = -1; if(tdb == NULL) errAbort("TrackDb entry null for perlegen, item=%s\n", item); genericHeader(tdb, item); printCustomUrl(tdb, item, FALSE); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name; /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); /* chop leading digits off name which should be in x/yyyyyy format */ name = strstr(bed->name, "/"); if(name == NULL) name = bed->name; else name++; /* determine number of SNPs required from score */ switch(bed->score) { case 1000: numSnpsReq = 0; break; case 650: numSnpsReq = 1; break; case 500: numSnpsReq = 2; break; case 250: numSnpsReq = 3; break; case 50: numSnpsReq = 4; break; } /* finish off report ... */ printf("<B>Block:</B> %s<BR>\n", name); printf("<B>Number of SNPs in block:</B> %d<BR>\n", bed->blockCount); printf("<B>Number of SNPs to represent block:</B> %d<BR>\n",numSnpsReq); printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); hFreeConn(&conn); } void haplotypeDetails(struct trackDb *tdb, char *item) { int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; if(tdb == NULL) errAbort("TrackDb entry null for haplotype, item=%s\n", item); genericHeader(tdb, item); printCustomUrl(tdb, item, TRUE); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); /* finish off report ... */ printf("<B>Block:</B> %s<BR>\n", bed->name); printf("<B>Number of SNPs in block:</B> %d<BR>\n", bed->blockCount); /* printf("<B>Number of SNPs to represent block:</B> %d<BR>\n",numSnpsReq);*/ printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); hFreeConn(&conn); } void mitoDetails(struct trackDb *tdb, char *item) { int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; int numSnpsReq = -1; if(tdb == NULL) errAbort("TrackDb entry null for mitoSnps, item=%s\n", item); genericHeader(tdb, item); printCustomUrl(tdb, item, TRUE); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name; /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); /* chop leading digits off name which should be in xx/yyyyyy format */ name = strstr(bed->name, "/"); if(name == NULL) name = bed->name; else name++; /* determine number of SNPs required from score */ switch(bed->score) { case 1000: numSnpsReq = 0; break; case 650: numSnpsReq = 1; break; case 500: numSnpsReq = 2; break; case 250: numSnpsReq = 3; break; case 50: numSnpsReq = 4; break; } /* finish off report ... */ printf("<B>Block:</B> %s<BR>\n", name); printf("<B>Number of SNPs in block:</B> %d<BR>\n", bed->blockCount); printf("<B>Number of SNPs to represent block:</B> %d<BR>\n",numSnpsReq); printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); hFreeConn(&conn); } void ancientRDetails(struct trackDb *tdb, char *item) { struct sqlConnection *conn = hAllocConn(database); char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct bed *bed = NULL; char query[512]; struct sqlResult *sr = NULL; char **row; boolean firstTime = TRUE; double ident = -1.0; struct ancientRref *ar = NULL; if(tdb == NULL) errAbort("TrackDb entry null for ancientR, item=%s\n", item); genericHeader(tdb, item); printCustomUrl(tdb, item, TRUE); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s'", table, item, seqName ); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name; /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); name = bed->name; /* get % identity from score */ ident = ((bed->score + 500.0)/1500.0)*100.0; /* finish off report ... */ printf("<h4><i>Joint Alignment</i></h4>"); printf("<B>ID:</B> %s<BR>\n", name); printf("<B>Number of aligned blocks:</B> %d<BR>\n", bed->blockCount); if( ident == 50.0 ) printf("<B>Percent identity of aligned blocks:</B> <= %g%%<BR>\n", ident); else printf("<B>Percent identity of aligned blocks:</B> %g%%<BR>\n", ident); printf("<h4><i>Human Sequence</i></h4>"); printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } /* look in associated table 'ancientRref' to get human/mouse alignment*/ sqlSafef(query, sizeof query, "select * from %sref where id = '%s'", table, item ); sr = sqlGetResult( conn, query ); while ((row = sqlNextRow(sr)) != NULL ) { ar = ancientRrefLoad(row); printf("<h4><i>Repeat</i></h4>"); printf("<B>Name:</B> %s<BR>\n", ar->name); printf("<B>Class:</B> %s<BR>\n", ar->class); printf("<B>Family:</B> %s<BR>\n", ar->family); /* print the aligned sequences in html on multiple rows */ htmlHorizontalLine(); printf("<i>human sequence on top, mouse on bottom</i><br><br>" ); htmlPrintJointAlignment( ar->hseq, ar->mseq, 80, bed->chromStart, bed->chromEnd, bed->strand ); } printTrackHtml(tdb); hFreeConn(&conn); } void doGcDetails(struct trackDb *tdb, char *itemName) /* Show details for gc percent */ { int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; struct gcPercent *gc; boolean hasBin; char table[HDB_MAX_TABLE_STRING]; cartWebStart(cart, database, "Percentage GC in 20,000 Base Windows (GC)"); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and chromStart = %d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { gc = gcPercentLoad(row + hasBin); printPos(gc->chrom, gc->chromStart, gc->chromEnd, NULL, FALSE, NULL); printf("<B>GC Percentage:</B> %3.1f%%<BR>\n", ((float)gc->gcPpt)/10); gcPercentFree(&gc); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void chuckHtmlStart(char *title) /* Prints the header appropriate for the title * passed in. Links html to chucks stylesheet for * easier maintaince */ { printf("<HTML>\n<HEAD>\n%s", getCspMetaHeader()); // FIXME blueStyle should not be absolute to genome-test and should be called by: // webIncludeResourceFile("blueStyle.css"); printf("<LINK REL=STYLESHEET TYPE=\"text/css\" href=\"http://genome-test.gi.ucsc.edu/style/blueStyle.css\" title=\"Chuck Style\">\n"); printf("<title>%s</title>\n</head><body bgcolor=\"#f3f3ff\">",title); } void chuckHtmlContactInfo() /* Writes out Chuck's email so people bother Chuck instead of Jim */ { puts("<br><br><span style='font-size:x-small;'><i>If you have comments and/or suggestions please email " "<a href=\"mailto:sugnet@soe.ucsc.edu\">sugnet@soe.ucsc.edu</a>.</span>\n"); } void abbr(char *s, char *fluff) /* Cut out fluff from s. */ { int len; s = strstr(s, fluff); if (s != NULL) { len = strlen(fluff); strcpy(s, s+len); } } void printTableHeaderName(char *name, char *clickName, char *url) /* creates a table to display a name vertically, * basically creates a column of letters */ { int i, length; char *header = cloneString(name); header = cloneString(header); subChar(header,'_',' '); length = strlen(header); if(url == NULL) url = cloneString(""); /* printf("<b>Name:</b> %s\t<b>clickName:</b> %s\n", name,clickName); */ if (strstr(clickName,name)) printf("<table border=0 cellspacing=0 cellpadding=0 bgcolor='#D9E4F8'>\n"); else printf("<table border=0 cellspacing=0 cellpadding=0>\n"); for(i = 0; i < length; i++) { if (header[i] == ' ') printf("<tr><td align=center> </td></tr>\n"); else { if (strstr(clickName,name)) printf("<tr><td align=center bgcolor='#D9E4F8'>"); else printf("<tr><td align=center>"); /* if we have a url, create a reference */ if (differentString(url,"")) printf("<a href=\"%s\" TARGET=_BLANK>%c</a>", url, header[i]); else printf("%c", header[i]); printf("</td></tr>"); } printf("\n"); } printf("</table>\n"); freez(&header); } struct sageExp *loadSageExps(char *tableName, struct bed *bedist) /* load the sage experiment data. */ { struct sqlConnection *sc = NULL; /* struct sqlConnection *sc = sqlConnectRemote("localhost", user, password, "hgFixed"); */ char query[256]; struct sageExp *seList = NULL, *se=NULL; char **row; struct sqlResult *sr = NULL; if(hTableExists(database, tableName)) sc = hAllocConn(database); else sc = hAllocConn("hgFixed"); sqlSafef(query, sizeof query,"select * from sageExp order by num"); sr = sqlGetResult(sc,query); while((row = sqlNextRow(sr)) != NULL) { se = sageExpLoad(row); slAddHead(&seList,se); } sqlFreeResult(&sr); hFreeConn(&sc); slReverse(&seList); return seList; } struct sage *loadSageData(char *table, struct bed* bedList) /* load the sage data by constructing a query based on the qNames of the bedList */ { struct sqlConnection *sc = NULL; struct dyString *query = newDyString(2048); struct sage *sgList = NULL, *sg=NULL; struct bed *bed=NULL; char **row; int count=0; struct sqlResult *sr = NULL; if(hTableExists(database, table)) sc = hAllocConn(database); else sc = hAllocConn("hgFixed"); sqlDyStringPrintf(query, "select * from sage where "); for(bed=bedList;bed!=NULL;bed=bed->next) { if (count++) { dyStringPrintf(query," or uni=%d ", atoi(bed->name + 3 )); } else { dyStringPrintf(query," uni=%d ", atoi(bed->name + 3)); } } sr = sqlGetResult(sc,query->string); while((row = sqlNextRow(sr)) != NULL) { sg = sageLoad(row); slAddHead(&sgList,sg); } sqlFreeResult(&sr); hFreeConn(&sc); slReverse(&sgList); freeDyString(&query); return sgList; } int sageBedWSListIndex(struct bed *bedList, int uni) /* find the index of a bed by the unigene identifier in a bed list */ { struct bed *bed; int count =0; char buff[128]; safef(buff, sizeof buff, "Hs.%d", uni); for(bed = bedList; bed != NULL; bed = bed->next) { if(sameString(bed->name,buff)) return count; count++; } errAbort("Didn't find the unigene tag %s",buff); return 0; } int sortSageByBedOrder(const void *e1, const void *e2) /* used by slSort to sort the sage experiment data using the order of the beds */ { const struct sage *s1 = *((struct sage**)e1); const struct sage *s2 = *((struct sage**)e2); return(sageBedWSListIndex(sageExpList,s1->uni) - sageBedWSListIndex(sageExpList,s2->uni)); } void printSageGraphUrl(struct sage *sgList) /* print out a url to a cgi script which will graph the results */ { struct sage *sg = NULL; if (sgList == NULL) return; printf("Please click "); printf("<a target=_blank href=\"../cgi-bin/sageVisCGI?"); for(sg = sgList; sg != NULL; sg = sg->next) { if(sg->next == NULL) printf("u=%d", sg->uni); else printf("u=%d&", sg->uni); } printf("&db=%s",database); printf("\">here</a>"); printf(" to see the data as a graph.\n"); } void printSageReference(struct sage *sgList, struct trackDb *tdb) { printf("%s", tdb->html); printTBSchemaLink(tdb); } void sagePrintTable(struct bed *bedList, char *itemName, struct trackDb *tdb) /* load up the sage experiment data using bed->qNames and display it as a table */ { struct sageExp *seList = NULL, *se =NULL; struct sage *sgList=NULL, *sg=NULL; int featureCount; int count=0; seList=loadSageExps("sageExp",bedList); sgList = loadSageData("sage", bedList); slSort(&sgList,sortSageByBedOrder); printSageReference(sgList, tdb); /* temporarily disable this link until debugged and fixed. Fan printSageGraphUrl(sgList); */ printf("<BR>\n"); for(sg=sgList; sg != NULL; sg = sg->next) { char buff[256]; safef(buff, sizeof buff, "Hs.%d", sg->uni); } featureCount= slCount(sgList); printf("<basefont size=-1>\n"); printf("<table cellspacing=0 style='border:1px solid black;'>\n"); printf("<tr>\n"); printf("<th align=center>Sage Experiment</th>\n"); printf("<th align=center>Tissue</th>\n"); printf("<th align=center colspan=%d valign=top>Uni-Gene Clusters<br>(<b>Median</b> [Ave ± Stdev])</th>\n",featureCount); printf("</tr>\n<tr><td> </td><td> </td>\n"); for(sg = sgList; sg != NULL; sg = sg->next) { char buff[32]; char url[256]; safef(buff, sizeof buff, "Hs.%d", sg->uni); printf("<td valign=top align=center>\n"); safef(url, sizeof url, "https://www.ncbi.nlm.nih.gov/SAGE/SAGEcid.cgi?cid=%d&org=Hs",sg->uni); printTableHeaderName(buff, itemName, url); printf("</td>"); } printf("</tr>\n"); /* for each experiment write out the name and then all of the values */ for(se=seList;se!=NULL;se=se->next) { char *tmp; tmp = strstr(se->exp,"_"); if(++count%2) printf("<tr>\n"); else printf("<tr bgcolor=\"#bababa\">\n"); printf("<td align=left>"); printf("%s</td>\n", tmp ? (tmp+1) : se->exp); printf("<td align=left>%s</td>\n", se->tissueType); for(sg=sgList; sg!=NULL; sg=sg->next) { if (sg->aves[se->num] == -1.0) printf("<td>N/A</td>"); else printf("<td> <b>%4.1f</b> <span style='font-size:x-small;'>[%.2f ± %.2f]</span></td>\n", sg->meds[se->num],sg->aves[se->num],sg->stdevs[se->num]); } printf("</tr>\n"); } printf("</table>\n"); } struct bed *bedWScoreLoadByChrom(char *table, char *chrom, int start, int end) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; struct bed *bedWS, *bedWSList = NULL; char **row; char query[256]; struct hTableInfo *hti = hFindTableInfo(database, seqName, table); if(hti == NULL) errAbort("Can't find table: (%s) %s", seqName, table); else if(hti && sameString(hti->startField, "tStart")) sqlSafef(query, sizeof(query), "select qName,tStart,tEnd from %s where tName='%s' and tStart < %u and tEnd > %u", table, seqName, winEnd, winStart); else if(hti && sameString(hti->startField, "chromStart")) sqlSafef(query, sizeof(query), "select name,chromStart,chromEnd from %s" " where chrom='%s' and chromStart < %u and chromEnd > %u", table, seqName, winEnd, winStart); else errAbort("%s doesn't have tStart or chromStart", table); sr = sqlGetResult(conn, query); while((row = sqlNextRow(sr)) != NULL) { AllocVar(bedWS); bedWS->name = cloneString(row[0]); bedWS->chromStart = sqlUnsigned(row[1]); bedWS->chromEnd = sqlUnsigned(row[2]); bedWS->chrom = cloneString(seqName); slAddHead(&bedWSList, bedWS); } slReverse(&bedWSList); sqlFreeResult(&sr); hFreeConn(&conn); return bedWSList; } /* Lowe Lab additions */ void doSageDataDisp(char *tableName, char *itemName, struct trackDb *tdb) { struct bed *sgList = NULL; int sgCount=0; chuckHtmlStart("Sage Data Requested"); printf("<h2>Sage Data for: %s %d-%d</h2>\n", seqName, winStart+1, winEnd); puts("<table cellpadding=0 cellspacing=0><tr><td>\n"); sgList = bedWScoreLoadByChrom(tableName, seqName, winStart, winEnd); sgCount = slCount(sgList); if(sgCount > 50) printf("<hr><p>That will create too big of a table, try creating a window with less than 50 elements.<hr>\n"); else { sageExpList = sgList; sagePrintTable(sgList, itemName, tdb); } printf("</td></tr></table>\n"); /*zeroBytes(buff,64); safe(buff, sizeof buff, "%d", winStart); cgiMakeHiddenVar("winStart", buff); zeroBytes(buff,64); safef(buff, sizeof buff, "%d", winEnd); cgiMakeHiddenVar("winEnd", buff); cgiMakeHiddenVar("db",database); printf("<br>\n");*/ chuckHtmlContactInfo(); } void makeGrayShades(struct hvGfx *hvg) /* Make eight shades of gray in display. */ { int i; for (i=0; i<=maxShade; ++i) { struct rgbColor rgb; int level = 255 - (255*i/maxShade); if (level < 0) level = 0; rgb.r = rgb.g = rgb.b = level; shadesOfGray[i] = hvGfxFindRgb(hvg, &rgb); } shadesOfGray[maxShade+1] = MG_RED; } void mgMakeColorGradient(struct memGfx *mg, struct rgbColor *start, struct rgbColor *end, int steps, Color *colorIxs) /* Make a color gradient that goes smoothly from start * to end colors in given number of steps. Put indices * in color table in colorIxs */ { double scale = 0, invScale; double invStep; int i; int r,g,b; steps -= 1; /* Easier to do the calculation in an inclusive way. */ invStep = 1.0/steps; for (i=0; i<=steps; ++i) { invScale = 1.0 - scale; r = invScale * start->r + scale * end->r; g = invScale * start->g + scale * end->g; b = invScale * start->b + scale * end->b; colorIxs[i] = mgFindColor(mg, r, g, b); scale += invStep; } } void makeRedGreenShades(struct memGfx *mg) /* Allocate the shades of Red, Green and Blue */ { static struct rgbColor black = {0, 0, 0}; static struct rgbColor red = {255, 0, 0}; mgMakeColorGradient(mg, &black, &red, maxRGBShade+1, shadesOfRed); exprBedColorsMade = TRUE; } char *altGraphXMakeImage(struct trackDb *tdb, struct altGraphX *ag) /* Create a drawing of splicing pattern. */ { MgFont *font = mgSmallFont(); int fontHeight = mgFontLineHeight(font); struct spaceSaver *ssList = NULL; struct hash *heightHash = NULL; int rowCount = 0; struct tempName gifTn; int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH )); int pixHeight = 0; struct hvGfx *hvg; int lineHeight = 0; double scale = 0; scale = (double)pixWidth/(ag->tEnd - ag->tStart); lineHeight = 2 * fontHeight +1; altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount); pixHeight = rowCount * lineHeight; trashDirFile(&gifTn, "hgc", "hgc", ".png"); hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE); makeGrayShades(hvg); hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight); altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1, ag->tStart, ag->tEnd, scale, font, MG_BLACK, shadesOfGray, "Dummy", NULL); hvGfxUnclip(hvg); hvGfxClose(&hvg); printf( "<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n", gifTn.forHtml, pixWidth, pixHeight); return cloneString(gifTn.forHtml); } char *agXStringForEdge(struct altGraphX *ag, int i) /* classify an edge as intron or exon */ { if(ag->vTypes[ag->edgeStarts[i]] == ggSoftStart || ag->vTypes[ag->edgeStarts[i]] == ggHardStart) return "exon"; else if (ag->vTypes[ag->edgeStarts[i]] == ggSoftEnd || ag->vTypes[ag->edgeStarts[i]] == ggHardEnd) return "intron"; else return "unknown"; } char *agXStringForType(enum ggVertexType t) /* convert a type to a string */ { switch (t) { case ggSoftStart: return "ss"; case ggHardStart: return "hs"; case ggSoftEnd: return "se"; case ggHardEnd: return "he"; default: return "NA"; } } void printAltGraphXEdges(struct altGraphX *ag) /* Print out at table showing all of the vertexes and edges of an altGraphX. */ { int i = 0, j = 0; printf("<table cellpadding=1 border=1>\n"); printf("</table>\n"); printf("<table cellpadding=0 cellspacing=0>\n"); printf("<tr><th><b>Vertices</b></th><th><b>Edges</b></th></tr>\n"); printf("<tr><td valign=top>\n"); printf("<table cellpadding=1 border=1>\n"); printf("<tr><th><b>Number</b></th><th><b>Type</b></th></tr>\n"); for(i=0; i<ag->vertexCount; i++) { printf("<tr><td>%d</td><td>%s</td></tr>\n", i, agXStringForType(ag->vTypes[i])); } printf("</table>\n"); printf("</td><td valign=top>\n"); printf("<table cellpadding=1 border=1>\n"); printf("<tr><th><b>Start</b></th><th><b>End</b></th><th><b>Type</b></th><th><b>Evidence</b></th></tr>\n"); for(i=0; i<ag->edgeCount; i++) { struct evidence *e = slElementFromIx(ag->evidence, i); printf("<tr><td>%d</td><td>%d</td>", ag->edgeStarts[i], ag->edgeEnds[i]); printf("<td><a href=\"%s&position=%s:%d-%d&mrna=full&intronEst=full&refGene=full&altGraphX=full\">%s</a></td><td>", hgTracksPathAndSettings(), ag->tName, ag->vPositions[ag->edgeStarts[i]], ag->vPositions[ag->edgeEnds[i]], agXStringForEdge(ag, i)); for(j=0; j<e->evCount; j++) printf("%s, ", ag->mrnaRefs[e->mrnaIds[j]]); printf("</td></tr>\n"); } printf("</table>\n"); } void doAltGraphXDetails(struct trackDb *tdb, char *item) /* do details page for an altGraphX */ { int id = atoi(item); char query[256]; struct altGraphX *ag = NULL; struct altGraphX *orthoAg = NULL; char buff[128]; struct sqlConnection *conn = hAllocConn(database); char *image = NULL; /* Load the altGraphX record and start page. */ if (id != 0) { sqlSafef(query, sizeof(query),"select * from %s where id=%d", tdb->table, id); ag = altGraphXLoadByQuery(conn, query); } else { sqlSafef(query, sizeof(query), "select * from %s where tName like '%s' and tStart <= %d and tEnd >= %d", tdb->table, seqName, winEnd, winStart); ag = altGraphXLoadByQuery(conn, query); } if (ag == NULL) errAbort("hgc::doAltGraphXDetails() - couldn't find altGraphX with id=%d", id); genericHeader(tdb, ag->name); printPosOnChrom(ag->tName, ag->tStart, ag->tEnd, ag->strand, FALSE, NULL); /* Print a display of the Graph. */ printf("<b>Plots of Alt-Splicing:</b>"); printf("<center>\n"); if(sameString(tdb->table, "altGraphXPsb2004")) printf("Common Splicing<br>"); printf("Alt-Splicing drawn to scale.<br>"); image = altGraphXMakeImage(tdb,ag); freez(&image); /* Normally just print graph with exons scaled up. For conserved track also display orthologous loci. */ if(differentString(tdb->table, "altGraphXPsb2004")) { struct altGraphX *copy = altGraphXClone(ag); altGraphXVertPosSort(copy); altGraphXEnlargeExons(copy); printf("<br>Alt-Splicing drawn with exons enlarged.<br>\n"); image = altGraphXMakeImage(tdb,copy); freez(&image); altGraphXFree(©); } else { struct sqlConnection *orthoConn = NULL; struct altGraphX *origAg = NULL; char *db2="mm3"; sqlSafef(query, sizeof(query), "select * from altGraphX where name='%s'", ag->name); origAg = altGraphXLoadByQuery(conn, query); puts("<br><center>Human</center>\n"); altGraphXMakeImage(tdb,origAg); orthoConn = hAllocConn(db2); sqlSafef(query, sizeof(query), "select orhtoAgName from orthoAgReport where agName='%s'", ag->name); sqlQuickQuery(conn, query, buff, sizeof(buff)); sqlSafef(query, sizeof(query), "select * from altGraphX where name='%s'", buff); orthoAg = altGraphXLoadByQuery(orthoConn, query); if(differentString(orthoAg->strand, origAg->strand)) { altGraphXReverseComplement(orthoAg); puts("<br>Mouse (opposite strand)\n"); } else puts("<br>Mouse\n"); printf("<a HREF=\"%s&db=%s&position=%s:%d-%d&mrna=squish&intronEst=squish&refGene=pack&altGraphX=full\"", hgTracksName(), "mm3", orthoAg->tName, orthoAg->tStart, orthoAg->tEnd); printf(" ALT=\"Zoom to browser coordinates of altGraphX\">"); printf("<span style='font-size:smaller;'>[%s.%s:%d-%d]</span></a><br><br>\n", "mm3", orthoAg->tName, orthoAg->tStart, orthoAg->tEnd); altGraphXMakeImage(tdb,orthoAg); } printf("<br><a HREF=\"%s&position=%s:%d-%d&mrna=full&intronEst=full&refGene=full&altGraphX=full\"", hgTracksPathAndSettings(), ag->tName, ag->tStart, ag->tEnd); printf(" ALT=\"Zoom to browser coordinates of Alt-Splice\">"); printf("Jump to browser for %s</a><span style='font-size:smaller;'> [%s:%d-%d] </span><br><br>\n", ag->name, ag->tName, ag->tStart, ag->tEnd); if(cgiVarExists("agxPrintEdges")) printAltGraphXEdges(ag); printf("</center>\n"); hFreeConn(&conn); } struct lineFile *openExtLineFile(unsigned int extFileId) /* Open line file corresponding to id in extFile table. */ { char *path = hExtFileName(database, "extFile", extFileId); struct lineFile *lf = lineFileOpen(path, TRUE); freeMem(path); return lf; } void printSampleWindow( struct psl *thisPsl, int thisWinStart, int thisWinEnd, char *winStr, char *otherOrg, char *otherDb, char *pslTableName ) { char otherString[256]; char pslItem[1024]; safef(pslItem, sizeof pslItem, "%s:%d-%d %s:%d-%d", thisPsl->qName, thisPsl->qStart, thisPsl->qEnd, thisPsl->tName, thisPsl->tStart, thisPsl->tEnd ); safef(otherString, sizeof otherString, "%d&pslTable=%s&otherOrg=%s&otherChromTable=%s&otherDb=%s", thisPsl->tStart, pslTableName, otherOrg, "chromInfo" , otherDb ); if (pslTrimToTargetRange(thisPsl, thisWinStart, thisWinEnd) != NULL) { hgcAnchorWindow("htcLongXenoPsl2", pslItem, thisWinStart, thisWinEnd, otherString, thisPsl->tName); printf("%s</A>\n", winStr ); } } void firstAndLastPosition( int *thisStart, int *thisEnd, struct psl *thisPsl ) /*return the first and last base of a psl record (not just chromStart * and chromEnd but the actual blocks.*/ { *thisStart = thisPsl->tStarts[0]; *thisEnd = thisPsl->tStarts[thisPsl->blockCount - 1]; if( thisPsl->strand[1] == '-' ) { *thisStart = thisPsl->tSize - *thisStart; *thisEnd = thisPsl->tSize - *thisEnd; } *thisEnd += thisPsl->blockSizes[thisPsl->blockCount - 1]; } boolean sampleClickRelevant( struct sample *smp, int i, int left, int right, int humMusWinSize, int thisStart, int thisEnd ) /* Decides if a sample is relevant for the current window and psl * record start and end positions */ { if ((smp->chromStart + smp->samplePosition[i] - humMusWinSize / 2 + 1) < left && (smp->chromStart + smp->samplePosition[i] + humMusWinSize / 2 ) < left ) return(0); if( smp->chromStart + smp->samplePosition[i] - humMusWinSize / 2 + 1 < thisStart && (smp->chromStart + smp->samplePosition[i] + humMusWinSize / 2 ) < thisStart ) return(0); if ((smp->chromStart + smp->samplePosition[i] - humMusWinSize / 2 + 1) > right && (smp->chromStart + smp->samplePosition[i] + humMusWinSize / 2 ) > right ) return(0); if( smp->chromStart + smp->samplePosition[i] - humMusWinSize / 2 + 1 > thisEnd && smp->chromStart + smp->samplePosition[i] + humMusWinSize / 2 > thisEnd ) return(0); return(1); } static double whichNum( double tmp, double min0, double max0, int n) /*gets range nums. from bin values*/ { return( (max0 - min0)/(double)n * tmp + min0 ); } void humMusSampleClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int smpSize, char *otherOrg, char *otherDb, char *pslTableName, boolean printWindowFlag ) /* Handle click in humMus sample (wiggle) track. */ { int humMusWinSize = 50; int i; char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct sample *smp; char query[512]; char tempTableName[1024]; struct sqlResult *sr; char **row; char **pslRow; boolean firstTime = TRUE; struct psl *thisPsl; char str[256]; char thisItem[256]; char otherString[256] = ""; struct sqlResult *pslSr; struct sqlConnection *conn2 = hAllocConn(database); int thisStart, thisEnd; int left = cartIntExp( cart, "l" ); int right = cartIntExp( cart, "r" ); char *winOn = cartUsualString( cart, "win", "F" ); if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s'", table, item, seqName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); smp = sampleLoad(row+hasBin); safef(tempTableName, sizeof tempTableName, "%s_%s", smp->chrom, pslTableName ); if (!hFindSplitTable(database, seqName, pslTableName, table, sizeof table, &hasBin)) errAbort("table %s not found", pslTableName); sqlSafef(query, sizeof query, "select * from %s where tName = '%s' and tEnd >= %d and tStart <= %d" , table, smp->chrom, smp->chromStart+smp->samplePosition[0] , smp->chromStart+smp->samplePosition[smp->sampleCount-1] ); pslSr = sqlGetResult(conn2, query); if(!sameString(winOn,"T")) { while(( pslRow = sqlNextRow(pslSr)) != NULL ) { thisPsl = pslLoad( pslRow+hasBin ); firstAndLastPosition( &thisStart, &thisEnd, thisPsl ); snprintf(thisItem, 256, "%s:%d-%d %s:%d-%d", thisPsl->qName, thisPsl->qStart, thisPsl->qEnd, thisPsl->tName, thisPsl->tStart, thisPsl->tEnd ); longXenoPsl1Given(tdb, thisItem, otherOrg, "chromInfo", otherDb, thisPsl, pslTableName ); safef(otherString, sizeof otherString, "%d&win=T", thisPsl->tStart ); hgcAnchorSomewhere( tdb->track, item, otherString, thisPsl->tName ); printf("View individual alignment windows\n</a>"); printf("<br><br>"); } } else { cartSetString( cart, "win", "F" ); printf("<h3>Alignments Windows </h3>\n" "<b>start stop" " L-score</b><br>" ); while(( pslRow = sqlNextRow(pslSr)) != NULL ) { thisPsl = pslLoad( pslRow+hasBin ); firstAndLastPosition( &thisStart, &thisEnd, thisPsl ); for( i=0; i<smp->sampleCount; i++ ) { if( !sampleClickRelevant( smp, i, left, right, humMusWinSize, thisStart, thisEnd ) ) continue; snprintf( str, 256, "%d %d %g<br>", max( smp->chromStart + smp->samplePosition[i] - humMusWinSize / 2 + 1, thisStart + 1), min(smp->chromStart + smp->samplePosition[i] + humMusWinSize / 2, thisEnd ), whichNum(smp->sampleHeight[i],0.0,8.0,1000) ); /* 0 to 8.0 is the fixed total L-score range for * all these conservation tracks. Scores outside * this range are truncated. */ printSampleWindow( thisPsl, smp->chromStart + smp->samplePosition[i] - humMusWinSize / 2, smp->chromStart + smp->samplePosition[i] + humMusWinSize / 2, str, otherOrg, otherDb, pslTableName ); } printf("<br>"); } } } } void footPrinterSampleClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int smpSize) /* Handle click in humMus sample (wiggle) track. */ { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct sample *smp; char query[512]; char tempTableName[1024]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; char filename[10000]; char pslTableName[128] = "blastzBestMouse"; int offset; int motifid; if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", table, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); smp = sampleLoad(row+hasBin); sscanf(smp->name,"footPrinter.%d.%d",&offset,&motifid); safef(filename, sizeof filename, "../zoo_blanchem/new_raw2_offset%d.fa.main.html?motifID=%d", offset, motifid); safef(tempTableName, sizeof tempTableName,"%s_%s", smp->chrom, pslTableName ); if (!hFindSplitTable(database, seqName, pslTableName, table, sizeof table, &hasBin)) errAbort("table %s not found", pslTableName); sqlSafef(query, sizeof query, "select * from %s where tName = '%s' and tEnd >= %d and tStart <= %d" , table, smp->chrom, smp->chromStart+smp->samplePosition[0], smp->chromStart+smp->samplePosition[smp->sampleCount-1] ); printf("Content-Type: text/html\n\n<HTML><BODY><SCRIPT>\n"); printf("location.replace('%s')\n",filename); printf("</SCRIPT> <NOSCRIPT> No JavaScript support. " "Click <b><a href=\"%s\">continue</a></b> for " "the requested GenBank report. </NOSCRIPT>\n", filename); } } void humMusClickHandler(struct trackDb *tdb, char *item, char *targetName, char *targetDb, char *targetTable, boolean printWindowFlag ) /* Put up sample track info. */ { char *words[16], *dupe = cloneString(tdb->type); int num; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); genericHeader(tdb, item); wordCount = chopLine(dupe, words); if (wordCount > 0) { num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; humMusSampleClick( conn, tdb, item, start, num, targetName, targetDb, targetTable, printWindowFlag ); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void footPrinterClickHandler(struct trackDb *tdb, char *item ) /* Put up generic track info. */ { char *words[16], *dupe = cloneString(tdb->type); int num; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); wordCount = chopLine(dupe, words); if (wordCount > 0) { num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; footPrinterSampleClick(conn, tdb, item, start, num); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void hgCustom(char *trackId, char *fileItem) /* Process click on custom track. */ { char *fileName, *itemName; struct customTrack *ctList = getCtList(); struct customTrack *ct; struct bed *bed = (struct bed *)NULL; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *item = cartString(cart, "i"); char *type; fileName = nextWord(&fileItem); for (ct = ctList; ct != NULL; ct = ct->next) if (sameString(trackId, ct->tdb->track)) break; if (ct == NULL) errAbort("Couldn't find '%s' in '%s'", trackId, fileName); type = ct->tdb->type; cartWebStart(cart, database, "Custom Track: %s", ct->tdb->shortLabel); itemName = skipLeadingSpaces(fileItem); printf("<H2>%s</H2>\n", ct->tdb->longLabel); if (sameWord(type, "array")) doExpRatio(ct->tdb, fileItem, ct); else if ( startsWith( "longTabix", type)) doLongTabix(ct->tdb, item); else if (sameWord(type, "encodePeak")) doEncodePeak(ct->tdb, ct, fileName); else if (sameWord(type, "bigNarrowPeak")) doBigEncodePeak(ct->tdb, NULL, item); else if (sameWord(type, "bigWig")) bigWigCustomClick(ct->tdb); else if (sameWord(type, "bigChain")) genericChainClick(NULL, ct->tdb, item, start, "seq"); else if (sameWord(type, "bigPsl")) genericBigPslClick(NULL, ct->tdb, item, start, end); else if (sameWord(type, "bigMaf")) genericMafClick(NULL, ct->tdb, item, start); else if (sameWord(type, "bigDbSnp")) doBigDbSnp(ct->tdb, item); else if (sameWord(type, "bigBed") || sameWord(type, "bigGenePred")) bigBedCustomClick(ct->tdb); else if (sameWord(type, "bigBarChart") || sameWord(type, "barChart")) doBarChartDetails(ct->tdb, item); else if (sameWord(type, "bigInteract") || sameWord(type, "interact")) doInteractDetails(ct->tdb, item); else if (sameWord(type, "bam")) doBamDetails(ct->tdb, itemName); else if (sameWord(type, "vcfTabix") || sameWord(type, "vcfPhasedTrio")) doVcfTabixDetails(ct->tdb, itemName); else if (sameWord(type, "vcf")) doVcfDetails(ct->tdb, itemName); else if (sameWord(type, "makeItems")) doMakeItemsDetails(ct, fileName); // fileName is first word, which is, go figure, id else if (ct->wiggle) { if (ct->dbTrack) { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); genericWiggleClick(conn, ct->tdb, fileItem, start); hFreeConn(&conn); } else genericWiggleClick(NULL, ct->tdb, fileItem, start); /* the NULL is for conn, don't need that for custom tracks */ } else if (ct->dbTrack && startsWith("bedGraph", ct->dbTrackType)) { printf("<P><A HREF=\"../cgi-bin/hgTables?db=%s&hgta_group=%s&hgta_track=%s" "&hgta_table=%s&position=%s:%d-%d&" "hgta_doSchema=describe+table+schema\" TARGET=_BLANK>" "View table schema</A></P>\n", database, ct->tdb->grp, ct->tdb->table, ct->tdb->table, seqName, winStart+1, winEnd); } else if (ct->dbTrack && sameString(ct->dbTrackType, "maf")) { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct sqlConnection *conn2 = hAllocConn(CUSTOM_TRASH); char *saveTable = ct->tdb->table; char *saveTrack = ct->tdb->track; ct->tdb->table = ct->tdb->track = ct->dbTableName; customMafClick(conn, conn2, ct->tdb); ct->tdb->table = saveTable; ct->tdb->track = saveTrack; hFreeConn(&conn2); hFreeConn(&conn); } else if (ct->dbTrack && sameWord(type, "bedDetail")) { doBedDetail(ct->tdb, ct, itemName); } else if (ct->dbTrack && sameWord(type, "pgSnp")) { doPgSnp(ct->tdb, itemName, ct); } else { if (ct->dbTrack) { char where[512]; int rowOffset; char **row; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct sqlResult *sr = NULL; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); sqlSafefFrag(where, sizeof(where), "chromStart = '%d' and chromEnd = '%d'", start, end); if (ct->fieldCount >= 4) { sqlSafefAppend(where, sizeof(where), " and name = '%s'", itemName); } sr = hRangeQuery(conn, ct->dbTableName, seqName, start, end, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { bedFree(&bed); bed = bedLoadN(row+rowOffset, ct->fieldCount); } sqlFreeResult(&sr); hFreeConn(&conn); } if (ct->fieldCount < 4) { if (! ct->dbTrack) { for (bed = ct->bedList; bed != NULL; bed = bed->next) if (bed->chromStart == start && sameString(seqName, bed->chrom)) break; } if (bed) printPos(bed->chrom, bed->chromStart, bed->chromEnd, NULL, TRUE, NULL); if (ct->dbTrack) printUpdateTime(CUSTOM_TRASH, ct->tdb, ct); printTrackHtml(ct->tdb); return; } else { if (! ct->dbTrack) { for (bed = ct->bedList; bed != NULL; bed = bed->next) if (bed->chromStart == start && sameString(seqName, bed->chrom)) if (bed->name == NULL || sameString(itemName, bed->name) ) break; } } if (bed == NULL) errAbort("Couldn't find %s@%s:%d in %s", itemName, seqName, start, fileName); printCustomUrl(ct->tdb, itemName, TRUE); bedPrintPos(bed, ct->fieldCount, NULL); } printTrackUiLink(ct->tdb); printUpdateTime(CUSTOM_TRASH, ct->tdb, ct); printTrackHtml(ct->tdb); } void blastProtein(struct trackDb *tdb, char *itemName) /* Show protein to translated dna alignment for accession. */ { char startBuf[64], endBuf[64]; int start = cartInt(cart, "o"); boolean isClicked; struct psl *psl = 0; struct sqlResult *sr = NULL; struct sqlConnection *conn = hAllocConn(database); char query[256], **row; struct psl* pslList = getAlignments(conn, tdb->table, itemName); char *useName = itemName; char *acc = NULL, *prot = NULL; char *gene = NULL, *pos = NULL; char *ptr; char *buffer; char *spAcc; boolean isCe = FALSE; boolean isDm = FALSE; boolean isSacCer = FALSE; char *pred = trackDbSettingOrDefault(tdb, "pred", "NULL"); char *blastRef = trackDbSettingOrDefault(tdb, "blastRef", "NULL"); if (sameString("blastSacCer1SG", tdb->table)) isSacCer = TRUE; if (startsWith("blastDm", tdb->table)) isDm = TRUE; if (startsWith("blastCe", tdb->table)) isCe = TRUE; buffer = needMem(strlen(itemName)+ 1); strcpy(buffer, itemName); acc = buffer; if (blastRef != NULL) { char *thisDb = cloneString(blastRef); char *table; if ((table = strchr(thisDb, '.')) != NULL) { *table++ = 0; if (hTableExists(thisDb, table)) { if (!isCe && (ptr = strchr(acc, '.'))) *ptr = 0; sqlSafef(query, sizeof(query), "select geneId, extra1, refPos from %s where acc = '%s'", blastRef, acc); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { useName = row[0]; prot = row[1]; pos = row[2]; } sqlFreeResult(&sr); } } } else if ((pos = strchr(acc, '.')) != NULL) { *pos++ = 0; if ((gene = strchr(pos, '.')) != NULL) { *gene++ = 0; useName = gene; if (!isDm && !isCe && ((prot = strchr(gene, '.')) != NULL)) *prot++ = 0; } } if (isDm == TRUE) cartWebStart(cart, database, "FlyBase Protein %s", useName); else if (isSacCer == TRUE) cartWebStart(cart, database, "Yeast Protein %s", useName); else if (isCe == TRUE) cartWebStart(cart, database, "C. elegans Protein %s", useName); else cartWebStart(cart, database, "Human Protein %s", useName); if (pos != NULL) { if (isDm == TRUE) { char *dmDb = cloneString(strchr(tdb->track, 'D')); *dmDb = tolower(*dmDb); *strchr(dmDb, 'F') = 0; printf("<B>D. melanogaster position:</B>\n"); printf("<A TARGET=_blank HREF=\"%s?position=%s&db=%s\">", hgTracksName(), pos, dmDb); } else if (isCe == TRUE) { char *assembly; if (sameString("blastWBRef01", tdb->table)) assembly = "ce3"; else if (sameString("blastCe9SG", tdb->table)) assembly = "ce9"; else if (sameString("blastCe6SG", tdb->table)) assembly = "ce6"; else if (sameString("blastCe4SG", tdb->table)) assembly = "ce4"; else assembly = "ce3"; printf("<B>C. elegans position:</B>\n"); printf("<A TARGET=_blank HREF=\"%s?position=%s&db=%s\">", hgTracksName(), pos, assembly); } else if (isSacCer == TRUE) { char *assembly = "sacCer1"; printf("<B>Yeast position:</B>\n"); printf("<A TARGET=_blank HREF=\"%s?position=%s&db=%s\">", hgTracksName(), pos, assembly); } else { char *assembly; if (sameString("blastHg16KG", tdb->table)) assembly = "hg16"; else if (sameString("blastHg17KG", tdb->table)) assembly = "hg17"; else assembly = "hg18"; printf("<B>Human position:</B>\n"); printf("<A TARGET=_blank HREF=\"%s?position=%s&db=%s\">", hgTracksName(), pos, assembly); } printf("%s</A><BR>",pos); } if (acc != NULL) { if (isDm== TRUE) printf("<B>FlyBase Entry:</B> <A HREF=\" %s%s", tdb->url, acc); else if (isSacCer== TRUE) printf("<B>SGD Entry:</B> <A HREF=\" %s%s", tdb->url, acc); else if (isCe == TRUE) printf("<B>Wormbase ORF Name:</B> <A HREF=\" %s%s", tdb->url, acc); else { printf("<B>Human mRNA:</B> <A HREF=\""); printEntrezNucleotideUrl(stdout, acc); } printf("\" TARGET=_blank>%s</A><BR>\n", acc); } if (!isDm && (prot != NULL) && !sameString("(null)", prot) && sqlTableExists(conn,"proteome.uniProtAlias")) { printf("<B>UniProtKB:</B> "); printf("<A HREF="); printSwissProtProteinUrl(stdout, prot); spAcc = uniProtFindPrimAcc(prot); if (spAcc == NULL) { printf(" TARGET=_blank>%s</A></B><BR>\n", prot); } else { printf(" TARGET=_blank>%s</A></B><BR>\n", spAcc); } } printf("<B>Protein length:</B> %d<BR>\n",pslList->qSize); slSort(&pslList, pslCmpMatch); if (slCount(pslList) > 1) printf("<P>The alignment you clicked on is first in the table below.<BR>\n"); printf("<TT><PRE>"); printf("ALIGNMENT PEPTIDE COVERAGE IDENTITY START END EXTENT STRAND LINK TO BROWSER \n"); printf("--------------------------------------------------------------------------------\n"); for (isClicked = 1; isClicked >= 0; isClicked -= 1) { for (psl = pslList; psl != NULL; psl = psl->next) { if (isPslToPrintByClick(psl, start, isClicked)) { printf("<A HREF=\"%s&o=%d&g=htcProteinAli&i=%s&c=%s&l=%d&r=%d&db=%s&aliTable=%s&pred=%s\">", hgcPathAndSettings(), psl->tStart, psl->qName, psl->tName, psl->tStart, psl->tEnd, database,tdb->track, pred); printf("alignment</A> "); printf("<A HREF=\"%s&o=%d&g=htcGetBlastPep&i=%s&c=%s&l=%d&r=%d&db=%s&aliTable=%s\">", hgcPathAndSettings(), psl->tStart, psl->qName, psl->tName, psl->tStart, psl->tEnd, database,tdb->track); printf("peptide</A> "); printf("%5.1f%% %5.1f%% %5d %5d %5.1f%% %c ", 100.0 * (psl->match + psl->repMatch + psl->misMatch) / psl->qSize, 100.0 * (psl->match + psl->repMatch) / (psl->match + psl->repMatch + psl->misMatch), psl->qStart+1, psl->qEnd, 100.0 * (psl->qEnd - psl->qStart) / psl->qSize, psl->strand[1]); printf("<A HREF=\"%s&position=%s:%d-%d&db=%s&ss=%s+%s\">", hgTracksPathAndSettings(), psl->tName, psl->tStart + 1, psl->tEnd, database, tdb->track, itemName); sprintLongWithCommas(startBuf, psl->tStart + 1); sprintLongWithCommas(endBuf, psl->tEnd); printf("%s:%s-%s</A> <BR>",psl->tName,startBuf, endBuf); if (isClicked) printf("\n"); } } } printf("</PRE></TT>"); /* Add description */ printTrackHtml(tdb); hFreeConn(&conn); } static void doSgdOther(struct trackDb *tdb, char *item) /* Display information about other Sacchromyces Genome Database * other (not-coding gene) info. */ { struct sqlConnection *conn = hAllocConn(database); struct dyString *dy = dyStringNew(1024); if (sqlTableExists(conn, "sgdOtherDescription")) { /* Print out description and type if available. */ struct sgdDescription sgd; struct sqlResult *sr; char query[256], **row; sqlSafef(query, sizeof(query), "select * from sgdOtherDescription where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { sgdDescriptionStaticLoad(row, &sgd); dyStringPrintf(dy, "<B>Description:</B> %s<BR>\n", sgd.description); dyStringPrintf(dy, "<B>Type:</B> %s<BR>\n", sgd.type); } sqlFreeResult(&sr); } hFreeConn(&conn); genericClickHandlerPlus(tdb, item, NULL, dy->string); dyStringFree(&dy); } void doPeptideAtlas(struct trackDb *tdb, char *item) /* PeptideAtlas item details display. Peptide details are in hgFixed.<table>Peptides */ { char query[512]; struct sqlResult *sr; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb, item); printCustomUrl(tdb, item, FALSE); struct sqlConnection *conn = hAllocConn(database); char peptideTable[128]; safef(peptideTable, sizeof(peptideTable), "%sPeptides", tdb->table); // peptide info struct sqlConnection *connFixed= hAllocConn("hgFixed"); if (sqlTableExists(connFixed, peptideTable)) { sqlSafef(query, sizeof(query), "select * from %s where accession = '%s'", peptideTable, item); sr = sqlGetResult(connFixed, query); row = sqlNextRow(sr); if (row != NULL) { struct peptideAtlasPeptide *peptideInfo; AllocVar(peptideInfo); peptideAtlasPeptideStaticLoad(row, peptideInfo); printf("<b>Peptide sequence:</b> %s<br>\n", peptideInfo->sequence); printf("<b>Peptide size:</b> %d<br>\n", (int)strlen(peptideInfo->sequence)); printf("<b>Samples where observed:</b> %d<br>\n", peptideInfo->sampleCount); printf("<b>Proteotypic score:</b> %.3f<br>\n", peptideInfo->proteotypicScore); printf("<b>Hydrophobicity:</b> %.3f<br><br>\n", peptideInfo->hydrophobicity); } sqlFreeResult(&sr); } hFreeConn(&connFixed); // peptide mappings sqlSafef(query, sizeof(query), "select * from %s where name = '%s' order by chrom, chromStart, chromEnd", tdb->table, item); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); struct bed *bed = NULL, *beds = NULL; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); while (row != NULL) { bed = bedLoadN(row + rowOffset, 12); if (sameString(bed->chrom, seqName) && bed->chromStart == start && bed->chromEnd == end) bedPrintPos(bed, 12, tdb); else slAddHead(&beds, bed); row = sqlNextRow(sr); } if (beds != NULL) { slSort(&beds, bedCmp); printf("<br><b>Other mappings of this peptide:</b> %d<br>\n", slCount(beds)); for (bed = beds; bed != NULL; bed = bed->next) { printf(" " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, bed->chrom, bed->chromStart+1, bed->chromEnd); printf("%s:%d-%d</A><BR>\n", bed->chrom, bed->chromStart+1, bed->chromEnd); } } hFreeConn(&conn); printTrackHtml(tdb); } static void doSgdClone(struct trackDb *tdb, char *item) /* Display information about other Sacchromyces Genome Database * other (not-coding gene) info. */ { struct sqlConnection *conn = hAllocConn(database); struct dyString *dy = dyStringNew(1024); if (sqlTableExists(conn, "sgdClone")) { /* print out url with ATCC number */ struct sgdClone sgd; struct sqlResult *sr; char query[256], **row; sqlSafef(query, sizeof(query), "select * from sgdClone where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { sgdCloneStaticLoad(row+1, &sgd); dyStringPrintf(dy, "<B>ATCC catalog number:</B><A HREF=\"http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=%s&Template=uniqueClones\" TARGET=_blank>%s</A><BR>\n", sgd.atccName, sgd.atccName); } sqlFreeResult(&sr); } hFreeConn(&conn); genericClickHandlerPlus(tdb, item, NULL, dy->string); dyStringFree(&dy); } static void doSimpleDiff(struct trackDb *tdb, char *otherOrg) /* Print out simpleDiff info. */ { struct simpleNucDiff snd; struct sqlConnection *conn = hAllocConn(database); char fullTable[HDB_MAX_TABLE_STRING]; char query[256], **row; struct sqlResult *sr; int rowOffset; int start = cartInt(cart, "o"); genericHeader(tdb, NULL); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &rowOffset)) errAbort("No %s table in database %s", tdb->table, database); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart=%d", fullTable, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { simpleNucDiffStaticLoad(row + rowOffset, &snd); printf("<B>%s sequence:</B> %s<BR>\n", hOrganism(database), snd.tSeq); printf("<B>%s sequence:</B> %s<BR>\n", otherOrg, snd.qSeq); bedPrintPos((struct bed*)&snd, 3, tdb); printf("<BR>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } static void doVntr(struct trackDb *tdb, char *item) /* Perfect microsatellite repeats from VNTR program (Gerome Breen). */ { struct vntr vntr; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; char extra[256]; int rowOffset = 0; int start = cartInt(cart, "o"); genericHeader(tdb, item); genericBedClick(conn, tdb, item, start, 4); safef(extra, sizeof(extra), "chromStart = %d", start); sr = hRangeQuery(conn, tdb->table, seqName, winStart, winEnd, extra, &rowOffset); if ((row = sqlNextRow(sr)) != NULL) { vntrStaticLoad(row + rowOffset, &vntr); printf("<B>Number of perfect repeats:</B> %.02f<BR>\n", vntr.repeatCount); printf("<B>Distance to last microsatellite repeat:</B> "); if (vntr.distanceToLast == -1) printf("n/a (first in chromosome)<BR>\n"); else printf("%d<BR>\n", vntr.distanceToLast); printf("<B>Distance to next microsatellite repeat:</B> "); if (vntr.distanceToNext == -1) printf("n/a (last in chromosome)<BR>\n"); else printf("%d<BR>\n", vntr.distanceToNext); if (isNotEmpty(vntr.forwardPrimer) && ! sameString("Design_Failed", vntr.forwardPrimer)) { printf("<B>Forward PCR primer:</B> %s<BR>\n", vntr.forwardPrimer); printf("<B>Reverse PCR primer:</B> %s<BR>\n", vntr.reversePrimer); printf("<B>PCR product length:</B> %s<BR>\n", vntr.pcrLength); } } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } static void doZdobnovSynt(struct trackDb *tdb, char *item) /* Gene homology-based synteny blocks from Zdobnov, Bork et al. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; char query[256]; int start = cartInt(cart, "o"); char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; genericHeader(tdb, item); genericBedClick(conn, tdb, item, start, 4); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", fullTable, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct zdobnovSynt *zd = zdobnovSyntLoad(row + hasBin); int l = cgiInt("l"); int r = cgiInt("r"); int i = 0; puts("<B>Homologous gene names in window:</B>"); for (i=0; i < zd->blockCount; i++) { int bStart = zd->chromStarts[i] + zd->chromStart; int bEnd = bStart + zd->blockSizes[i]; if (bStart <= r && bEnd >= l) { printf(" %s", zd->geneNames[i]); } } puts(""); zdobnovSyntFree(&zd); } else errAbort("query returned no results: \"%s\"", query); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } static void doDeweySynt(struct trackDb *tdb, char *item) /* Gene homology-based synteny blocks from Dewey, Pachter. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; struct bed *bed = NULL; char query[512]; genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d", fullTable, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { char *words[4]; int wordCount = 0; bed = bedLoad6(row+hasBin); bedPrintPos(bed, 4, tdb); printf("<B>Strand:</B> %s<BR>\n", bed->strand); wordCount = chopByChar(bed->name, '.', words, ArraySize(words)); if (wordCount == 3 && hDbExists(words[1])) { char *otherOrg = hOrganism(words[1]); printf("<A TARGET=\"_blank\" HREF=\"%s?db=%s&position=%s\">", hgTracksName(), words[1], cgiEncode(words[2])); printf("Open %s browser</A> at %s.<BR>\n", otherOrg, words[2]); } bedFree(&bed); } else errAbort("query returned no results: \"%s\"", query); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doScaffoldEcores(struct trackDb *tdb, char *item) /* Creates details page and gets the scaffold co-ordinates for unmapped */ /* genomes for display and to use to create the correct outside link URL */ { char *dupe, *words[16]; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); int num; struct bed *bed = NULL; char query[512]; struct sqlResult *sr; char **row; char *scaffoldName; int scaffoldStart, scaffoldEnd; struct dyString *itemUrl = newDyString(128), *d; char *old = "_"; char *new = ""; char *pat = "fold"; int hasBin = 1; dupe = cloneString(tdb->type); chopLine(dupe,words); /* get bed size */ num = 0; num = atoi(words[1]); /* get data for this item */ sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chromStart = %d", tdb->table, item, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) bed = bedLoadN(row+hasBin, num); genericHeader(tdb, item); /* convert chromosome co-ordinates to scaffold position and */ /* make into item for URL */ if (hScaffoldPos(database, bed->chrom, bed->chromStart, bed->chromEnd, &scaffoldName, &scaffoldStart, &scaffoldEnd) ) { scaffoldStart += 1; dyStringPrintf(itemUrl, "%s:%d-%d", scaffoldName, scaffoldStart, scaffoldEnd); /* remove underscore in scaffold name and change to "scafN" */ d = dyStringSub(itemUrl->string, old, new); itemUrl = dyStringSub(d->string, pat, new); printCustomUrl(tdb, itemUrl->string, TRUE); } genericBedClick(conn, tdb, item, start, num); printTrackHtml(tdb); dyStringFree(&itemUrl); freez(&dupe); sqlFreeResult(&sr); hFreeConn(&conn); } char *stripBDGPSuffix(char *name) /* cloneString(name), and if it ends in -R[A-Z], strip that off. */ { char *stripped = cloneString(name); int len = strlen(stripped); if (stripped[len-3] == '-' && stripped[len-2] == 'R' && isalpha(stripped[len-1])) stripped[len-3] = 0; return(stripped); } static void doGencodeIntron(struct trackDb *tdb, char *item) /* Intron validation from ENCODE Gencode/Havana gene predictions */ { struct sqlConnection *conn = hAllocConn(database); int start = cartInt(cart, "o"); struct gencodeIntron *intron, *intronList = NULL; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); genericHeader(tdb, item); sqlSafef(query, sizeof query, "select * from %s where name='%s' and chrom='%s' and chromStart=%d", tdb->table, item, seqName, start); intronList = gencodeIntronLoadByQuery(conn, query, rowOffset); for (intron = intronList; intron != NULL; intron = intron->next) { printf("<B>Intron:</B> %s<BR>\n", intron->name); printf("<B>Status:</B> %s<BR>\n", intron->status); printf("<B>Gene:</B> %s<BR>\n", intron->geneId); printf("<B>Transcript:</B> %s<BR>\n", intron->transcript); printPos(intron->chrom, intron->chromStart, intron->chromEnd, intron->strand, TRUE, intron->name); } hFreeConn(&conn); printTrackHtml(tdb); } static void printESPDetails(char **row, struct trackDb *tdb) /* Print details from a cell line subtrack table of encodeStanfordPromoters. */ { struct encodeStanfordPromoters *esp = encodeStanfordPromotersLoad(row); bedPrintPos((struct bed *)esp, 6, tdb); printf("<B>Gene model ID:</B> %s<BR>\n", esp->geneModel); printf("<B>Gene description:</B> %s<BR>\n", esp->description); printf("<B>Luciferase signal A:</B> %d<BR>\n", esp->lucA); printf("<B>Renilla signal A:</B> %d<BR>\n", esp->renA); printf("<B>Luciferase signal B:</B> %d<BR>\n", esp->lucB); printf("<B>Renilla signal B:</B> %d<BR>\n", esp->renB); printf("<B>Average Luciferase/Renilla Ratio:</B> %g<BR>\n", esp->avgRatio); printf("<B>Normalized Luciferase/Renilla Ratio:</B> %g<BR>\n", esp->normRatio); printf("<B>Normalized and log2 transformed Luciferase/Renilla Ratio:</B> %g<BR>\n", esp->normLog2Ratio); } static void printESPAverageDetails(char **row, struct trackDb *tdb) /* Print details from the averaged subtrack table of encodeStanfordPromoters. */ { struct encodeStanfordPromotersAverage *esp = encodeStanfordPromotersAverageLoad(row); bedPrintPos((struct bed *)esp, 6, tdb); printf("<B>Gene model ID:</B> %s<BR>\n", esp->geneModel); printf("<B>Gene description:</B> %s<BR>\n", esp->description); printf("<B>Normalized and log2 transformed Luciferase/Renilla Ratio:</B> %g<BR>\n", esp->normLog2Ratio); } void doEncodeStanfordPromoters(struct trackDb *tdb, char *item) /* Print ENCODE Stanford Promoters data. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; int start = cartInt(cart, "o"); char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; char query[1024]; cartWebStart(cart, database, "%s", tdb->longLabel); genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and name = '%s'", fullTable, seqName, start, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if (endsWith(tdb->table, "Average")) printESPAverageDetails(row+hasBin, tdb); else printESPDetails(row+hasBin, tdb); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doEncodeStanfordRtPcr(struct trackDb *tdb, char *item) /* Print ENCODE Stanford RTPCR data. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; int start = cartInt(cart, "o"); char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; char query[1024]; cartWebStart(cart, database, "%s", tdb->longLabel); genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and name = '%s'", fullTable, seqName, start, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct bed *bed = bedLoadN(row+hasBin, 5); bedPrintPos(bed, 5, tdb); printf("<B>Primer pair ID:</B> %s<BR>\n", row[hasBin+5]); printf("<B>Count:</B> %s<BR>\n", row[hasBin+6]); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doEncodeHapMapAlleleFreq(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct encodeHapMapAlleleFreq alleleFreq; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { encodeHapMapAlleleFreqStaticLoad(row+rowOffset, &alleleFreq); printf("<B>Variant:</B> %s<BR>\n", alleleFreq.otherAllele); printf("<B>Reference:</B> %s<BR>\n", alleleFreq.refAllele); bedPrintPos((struct bed *)&alleleFreq, 3, tdb); printf("<B>Reference Allele Frequency:</B> %f <BR>\n", alleleFreq.refAlleleFreq); printf("<B>Other Allele Frequency:</B> %f <BR>\n", alleleFreq.otherAlleleFreq); printf("<B>Center:</B> %s <BR>\n", alleleFreq.center); printf("<B>Total count:</B> %d <BR>\n", alleleFreq.totalCount); printf("-----------------------------------------------------<BR>\n"); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void showHapmapMonomorphic(struct hapmapAllelesSummary *summaryItem) { if (summaryItem->totalAlleleCountCEU > 0) { printf("<TR>"); printf("<TD>CEU</TD>"); printf("<TD bgcolor = \"lightgrey\">%d (100%%)</TD>", summaryItem->totalAlleleCountCEU); printf("</TR>\n"); } else printf("<TR><TD>CEU</TD><TD>not available</TD></TR>\n"); if (summaryItem->totalAlleleCountCHB > 0) { printf("<TR>"); printf("<TD>CHB</TD>"); printf("<TD bgcolor = \"lightgrey\">%d (100%%)</TD>", summaryItem->totalAlleleCountCHB); printf("</TR>\n"); } else printf("<TR><TD>CHB</TD><TD>not available</TD></TR>\n"); if (summaryItem->totalAlleleCountJPT > 0) { printf("<TR>"); printf("<TD>JPT</TD>"); printf("<TD bgcolor = \"lightgrey\">%d (100%%)</TD>", summaryItem->totalAlleleCountJPT); printf("</TR>\n"); } else printf("<TR><TD>JPT</TD><TD>not available</TD></TR>\n"); if (summaryItem->totalAlleleCountYRI > 0) { printf("<TR>"); printf("<TD>YRI</TD>"); printf("<TD bgcolor = \"lightgrey\">%d (100%%)</TD>", summaryItem->totalAlleleCountYRI); printf("</TR>\n"); } else printf("<TR><TD>YRI</TD><TD>not available</TD></TR>\n"); } void showOneHapmapRow(char *pop, char *allele1, char *allele2, char *majorAllele, int majorCount, int totalCount) { int count1 = 0; int count2 = 0; float freq1 = 0.0; float freq2 = 0.0; if (majorCount == 0) { printf("<TR><TD>%s</TD><TD align=center>-</TD><TD align=center>-</TD></TR>\n", pop); return; } if (sameString(allele1, majorAllele)) { count1 = majorCount; count2 = totalCount - majorCount; } else { count2 = majorCount; count1 = totalCount - majorCount; } freq1 = 100.0 * count1 / totalCount; freq2 = 100.0 * count2 / totalCount; printf("<TR>"); printf("<TD>%s</TD>", pop); if (count1 > count2) { printf("<TD bgcolor = \"lightgrey\" align=right>%d (%3.2f%%)</TD>", count1, freq1); printf("<TD align=right>%d (%3.2f%%)</TD>", count2, freq2); } else if (count1 < count2) { printf("<TD align=right>%d (%3.2f%%)</TD>", count1, freq1); printf("<TD bgcolor = \"lightgrey\" align=right>%d (%3.2f%%)</TD>", count2, freq2); } else { printf("<TD align=right>%d (%3.2f%%)</TD>", count1, freq1); printf("<TD align=right>%d (%3.2f%%)</TD>", count2, freq2); } printf("</TR>\n"); } void showHapmapAverageRow(char *label, float freq1) { float freq2 = 1.0 - freq1; printf("<TR><TD>%s</TD>", label); if (freq1 > 0.5) { printf("<TD bgcolor = \"lightgrey\" align=right>(%3.2f%%)</TD>", freq1*100); printf("<TD align=right>(%3.2f%%)</TD>", freq2*100); } else if (freq1 < 0.5) { printf("<TD align=right>(%3.2f%%)</TD>", freq1*100); printf("<TD bgcolor = \"lightgrey\" align=right>(%3.2f%%)</TD>", freq2*100); } else { printf("<TD align=right>(%3.2f%%)</TD>", freq1*100); printf("<TD align=right>(%3.2f%%)</TD>", freq2*100); } printf("</TR>\n"); } void doHapmapSnpsSummaryTable(struct sqlConnection *conn, struct trackDb *tdb, char *itemName, boolean showOrtho) /* Use the hapmapAllelesSummary table (caller checks for existence) to display allele * frequencies for the 4 HapMap Phase II populations. */ { char *table = tdb->table; struct hapmapAllelesSummary *summaryItem; struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); float het = 0.0; sqlSafef(query, sizeof(query), "select * from hapmapAllelesSummary where chrom = '%s' and " "chromStart=%d and name = '%s'", seqName, start, itemName); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); summaryItem = hapmapAllelesSummaryLoad(row+rowOffset); printf("<BR><B>Allele frequencies in each population (major allele highlighted):</B><BR>\n"); printf("<TABLE BORDER=1>\n"); if (differentString(summaryItem->allele2, "none")) { printf("<TR><TH>Population</TH> <TH>%s</TH> <TH>%s</TH></TR>\n", summaryItem->allele1, summaryItem->allele2); showOneHapmapRow("CEU", summaryItem->allele1, summaryItem->allele2, summaryItem->majorAlleleCEU, summaryItem->majorAlleleCountCEU, summaryItem->totalAlleleCountCEU); showOneHapmapRow("CHB", summaryItem->allele1, summaryItem->allele2, summaryItem->majorAlleleCHB, summaryItem->majorAlleleCountCHB, summaryItem->totalAlleleCountCHB); showOneHapmapRow("JPT", summaryItem->allele1, summaryItem->allele2, summaryItem->majorAlleleJPT, summaryItem->majorAlleleCountJPT, summaryItem->totalAlleleCountJPT); showOneHapmapRow("YRI", summaryItem->allele1, summaryItem->allele2, summaryItem->majorAlleleYRI, summaryItem->majorAlleleCountYRI, summaryItem->totalAlleleCountYRI); } else { printf("<TR><TH>Population</TH> <TH>%s</TH></TR>\n", summaryItem->allele1); showHapmapMonomorphic(summaryItem); } printf("</TABLE>\n"); het = summaryItem->score / 10.0; printf("<BR><B>Expected Heterozygosity (from total allele frequencies):</B> %3.2f%%<BR>\n", het); if (showOrtho && (differentString(summaryItem->chimpAllele, "none") || differentString(summaryItem->macaqueAllele, "none"))) { printf("<BR><B>Orthologous alleles:</B><BR>\n"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>Species</TH> <TH>Allele</TH> <TH>Quality Score</TH></TR>\n"); if (differentString(summaryItem->chimpAllele, "none")) { printf("<TR>"); printf("<TD>Chimp</TD>"); printf("<TD>%s</TD>", summaryItem->chimpAllele); printf("<TD>%d</TD>", summaryItem->chimpAlleleQuality); printf("</TR>"); } if (differentString(summaryItem->macaqueAllele, "none")) { printf("<TR>"); printf("<TD>Macaque</TD>"); printf("<TD>%s</TD>", summaryItem->macaqueAllele); printf("<TD>%d</TD>", summaryItem->macaqueAlleleQuality); printf("</TR>"); } printf("</TABLE>\n"); } sqlFreeResult(&sr); } void doHapmapSnpsAllPops(struct sqlConnection *conn, struct trackDb *tdb, char *itemName, boolean showOrtho) /* Show item's SNP allele frequencies for each of the 11 HapMap Phase III * populations, as well as chimp and macaque if showOrtho. */ { int i; printf("<BR><B>Allele frequencies in each population (major allele highlighted):</B><BR>\n"); printf("<TABLE BORDER=1>\n"); // Do a first pass to gather up alleles and counts: char *majorAlleles[HAP_PHASEIII_POPCOUNT]; int majorCounts[HAP_PHASEIII_POPCOUNT], haploCounts[HAP_PHASEIII_POPCOUNT]; int totalA1Count = 0, totalA2Count = 0, totalHaploCount = 0; float sumHet = 0.0; int sumA1A1 = 0, sumA1A2 = 0, sumA2A2 = 0; int popCount = 0; char *allele1 = NULL, *allele2 = NULL; for (i=0; i < HAP_PHASEIII_POPCOUNT; i++) { char *popCode = hapmapPhaseIIIPops[i]; struct hapmapSnps *item = NULL; char table[HDB_MAX_TABLE_STRING]; safef(table, sizeof(table), "hapmapSnps%s", popCode); if (sqlTableExists(conn, table)) { char query[512]; sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s'", table, itemName, seqName); struct sqlResult *sr = sqlGetResult(conn, query); char **row; if ((row = sqlNextRow(sr)) != NULL) { int rowOffset = hOffsetPastBin(database, seqName, table); item = hapmapSnpsLoad(row+rowOffset); } sqlFreeResult(&sr); } majorAlleles[i] = ""; majorCounts[i] = 0; haploCounts[i] = 0; if (item != NULL) { majorAlleles[i] = item->allele1; majorCounts[i] = 2*item->homoCount1 + item->heteroCount; if (item->homoCount1 < item->homoCount2) { majorAlleles[i] = item->allele2; majorCounts[i] = 2*item->homoCount2 + item->heteroCount; } haploCounts[i] = 2*(item->homoCount1 + item->homoCount2 + item->heteroCount); if (allele1 == NULL) { allele1 = item->allele1; allele2 = item->allele2; } else if (!sameString(allele1, item->allele1) || (isNotEmpty(allele2) && isNotEmpty(item->allele2) && !sameString(allele2, item->allele2))) warn("Allele order in hapmapSnps%s (%s/%s) is different from earlier table(s) (%s/%s)", popCode, item->allele1, item->allele2, allele1, allele2); totalA1Count += 2*item->homoCount1 + item->heteroCount; totalA2Count += 2*item->homoCount2 + item->heteroCount; totalHaploCount += haploCounts[i]; sumHet += ((float)item->heteroCount / (item->homoCount1 + item->homoCount2 + item->heteroCount)); sumA1A1 += item->homoCount1; sumA1A2 += item->heteroCount; sumA2A2 += item->homoCount2; popCount++; } } printf("<TR><TH>Population</TH> <TH>%s</TH> <TH>%s</TH></TR>\n", allele1, allele2); for (i=0; i < HAP_PHASEIII_POPCOUNT; i++) showOneHapmapRow(hapmapPhaseIIIPops[i], allele1, allele2, majorAlleles[i], majorCounts[i], haploCounts[i]); showHapmapAverageRow("Average", (float)totalA1Count / totalHaploCount); printf("</TABLE>\n"); printf("<BR><B>Average of populations' observed heterozygosities:</B> %3.2f%%<BR>\n", (100.0 * sumHet/popCount)); if (showOrtho) { boolean showedHeader = FALSE; int i; for (i = 0; hapmapOrthoSpecies[i] != NULL; i++) { char table[HDB_MAX_TABLE_STRING]; safef(table, sizeof(table), "hapmapAlleles%s", hapmapOrthoSpecies[i]); if (sqlTableExists(conn, table)) { if (!showedHeader) { printf("<BR><B>Orthologous alleles from reference genome assemblies:</B><BR>\n"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>Species</TH> <TH>Allele</TH> <TH>Quality Score</TH></TR>\n"); showedHeader = TRUE; } char query[512]; sqlSafef(query, sizeof(query), "select orthoAllele, score, strand from %s where name = '%s' and chrom = '%s'", table, itemName, seqName); struct sqlResult *sr = sqlGetResult(conn, query); char **row; if ((row = sqlNextRow(sr)) != NULL) { char *allele = row[0]; char *qual = row[1]; char *strand = row[2]; if (sameString("-", strand)) reverseComplement(allele, strlen(allele)); printf("<TR><TD>%s</TD><TD>%s</TD><TD>%s</TD></TR>", hapmapOrthoSpecies[i], allele, qual); } else printf("<TR><TD>%s</TD><TD>N/A</TD><TD>N/A</TD></TR>", hapmapOrthoSpecies[i]); sqlFreeResult(&sr); } } if (showedHeader) printf("</TABLE>\n"); } } void doHapmapSnpsSummary(struct sqlConnection *conn, struct trackDb *tdb, char *itemName, boolean showOrtho) /* Display per-population allele frequencies. */ { boolean isPhaseIII = sameString(trackDbSettingOrDefault(tdb, "hapmapPhase", "II"), "III"); if (!isPhaseIII && sqlTableExists(conn, "hapmapAllelesSummary")) doHapmapSnpsSummaryTable(conn, tdb, itemName, showOrtho); else doHapmapSnpsAllPops(conn, tdb, itemName, showOrtho); } void doHapmapSnps(struct trackDb *tdb, char *itemName) /* assume just one hapmap snp at a given location */ { char *table = tdb->table; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); int majorCount = 0; int minorCount = 0; char *majorAllele = NULL; char *minorAllele = NULL; char popCode[4]; safencpy(popCode, sizeof(popCode), table + strlen("hapmapSnps"), 3); popCode[3] = '\0'; genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); struct hapmapSnps *item = hapmapSnpsLoad(row+rowOffset); printf("<B>SNP rsId:</B> "); printDbSnpRsUrl(itemName, "%s", itemName); puts("<BR>"); printf("<B>Position:</B> <A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A><BR>\n", hgTracksPathAndSettings(), database, item->chrom, item->chromStart+1, item->chromEnd, item->chrom, item->chromStart+1, item->chromEnd); printf("<B>Strand:</B> %s<BR>\n", item->strand); printf("<B>Polymorphism type:</B> %s<BR>\n", item->observed); if (item->homoCount1 >= item->homoCount2) { majorAllele = cloneString(item->allele1); majorCount = item->homoCount1; minorCount = item->homoCount2; minorAllele = cloneString(item->allele2); } else { majorAllele = cloneString(item->allele2); majorCount = item->homoCount2; minorCount = item->homoCount1; minorAllele = cloneString(item->allele1); } printf("<BR><B>Genotype counts for %s:</B><BR>\n", popCode); printf("<TABLE BORDER=1>\n"); printf("<TR><TD>Major allele (%s) homozygotes</TD><TD align=right>%d individuals</TD></TR>\n", majorAllele, majorCount); if (minorCount > 0) printf("<TR><TD>Minor allele (%s) homozygotes</TD><TD align=right>%d individuals</TD></TR>\n", minorAllele, minorCount); if (item->heteroCount > 0) printf("<TR><TD>Heterozygotes (%s)</TD><TD align=right>%d individuals</TD></TR>\n", item->observed, item->heteroCount); printf("<TR><TD>Total</TD><TD align=right>%d individuals</TD></TR>\n", majorCount + minorCount + item->heteroCount); printf("</TABLE>\n"); sqlFreeResult(&sr); /* Show allele frequencies for all populations */ doHapmapSnpsSummary(conn, tdb, itemName, TRUE); printTrackHtml(tdb); hFreeConn(&conn); } void doHapmapOrthos(struct trackDb *tdb, char *itemName) /* could assume just one match */ { char *table = tdb->table; struct hapmapAllelesOrtho *ortho; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); char *otherDb = NULL; char *otherDbName = NULL; genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { ortho = hapmapAllelesOrthoLoad(row+rowOffset); printf("<B>Human Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, ortho->chrom, ortho->chromStart+1, ortho->chromEnd); printf("%s:%d-%d</A><BR>\n", ortho->chrom, ortho->chromStart+1, ortho->chromEnd); printf("<B>Human Strand: </B> %s\n", ortho->strand); printf("<BR>"); printf("<B>Polymorphism type:</B> %s<BR>\n", ortho->observed); if (startsWith("hapmapAllelesChimp", table)) { otherDb = "panTro2"; otherDbName = "Chimp"; } if (startsWith("hapmapAllelesMacaque", table)) { otherDb = "rheMac2"; otherDbName = "Macaque"; } printf("<B>%s </B>", otherDbName); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), otherDb, ortho->orthoChrom, ortho->orthoStart, ortho->orthoEnd); linkToOtherBrowser(otherDb, ortho->orthoChrom, ortho->orthoStart, ortho->orthoEnd); printf("%s:%d-%d</A><BR>\n", ortho->orthoChrom, ortho->orthoStart+1, ortho->orthoEnd); printf("<B>%s </B>", otherDbName); printf("<B>Strand:</B> %s\n", ortho->orthoStrand); printf("<BR>"); printf("<B>%s </B>", otherDbName); printf("<B>Allele:</B> %s\n", ortho->orthoAllele); printf("<BR>"); printf("<B>%s </B>", otherDbName); printf("<B>Allele Quality (0-100):</B> %d\n", ortho->score); } printf("<BR>\n"); /* get summary data (allele frequencies) here */ /* don't repeat ortho display */ doHapmapSnpsSummary(conn, tdb, itemName, FALSE); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void printSnpAllele(char *orthoDb, int snpVersion, char *rsId) /* check whether snpAlleles exists for a database */ /* if found, print value */ { char tableName[512]; struct sqlConnection *conn = sqlConnect(orthoDb); char query[256]; struct sqlResult *sr; char **row = NULL; safef(tableName, sizeof(tableName), "snp%d%sorthoAllele", snpVersion, database); if (!hTableExists(orthoDb, tableName)) { sqlDisconnect(&conn); return; } sqlSafef(query, sizeof(query), "select allele from %s where name = '%s'", tableName, rsId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (!row) { sqlDisconnect(&conn); return; } printf("<B>%s Allele:</B> %s<BR>\n", orthoDb, row[0]); sqlFreeResult(&sr); sqlDisconnect(&conn); } static char *fbgnFromCg(char *cgId) /* Given a BDGP ID, looks up its FBgn ID because FlyBase query no longer * supports BDGP IDs. Returns NULL if not found. * Do not free the statically allocated result. */ { static char result[32]; /* Ample -- FBgn ID's are 11 chars long. */ char query[512]; if (hTableExists(database, "flyBase2004Xref")) sqlSafef(query, sizeof(query), "select fbgn from flyBase2004Xref where name = '%s';", cgId); else if (hTableExists(database, "bdgpGeneInfo")) sqlSafef(query, sizeof(query), "select flyBaseId from bdgpGeneInfo where bdgpName = '%s';", cgId); else return NULL; struct sqlConnection *conn = hAllocConn(database); char *resultOrNULL = sqlQuickQuery(conn, query, result, sizeof(result)); hFreeConn(&conn); return resultOrNULL; } static void doPscreen(struct trackDb *tdb, char *item) /* P-Screen (BDGP Gene Disruption Project) P el. insertion locations/genes. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; char query[512]; genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", tdb->table); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and name = '%s'", fullTable, seqName, start, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct pscreen *psc = pscreenLoad(row+hasBin); int i; printCustomUrl(tdb, psc->name, FALSE); printPosOnChrom(psc->chrom, psc->chromStart, psc->chromEnd, psc->strand, FALSE, psc->name); if (psc->stockNumber != 0) printf("<B>Stock number:</B> " "<A HREF=\"http://flystocks.bio.indiana.edu/Reports/%d.html\" " "TARGET=_BLANK>%d</A><BR>\n", psc->stockNumber, psc->stockNumber); for (i=0; i < psc->geneCount; i++) { char gNum[4]; if (psc->geneCount > 1) safef(gNum, sizeof(gNum), " %d", i+1); else gNum[0] = 0; if (isNotEmpty(psc->geneIds[i])) { char *idType = "FlyBase"; char *fbgnId = psc->geneIds[i]; if (isBDGPName(fbgnId)) { char *stripped = stripBDGPSuffix(psc->geneIds[i]); idType = "BDGP"; fbgnId = fbgnFromCg(stripped); } if (fbgnId == NULL) printf("<B>Gene%s %s ID:</B> %s<BR>\n", gNum, idType, psc->geneIds[i]); else printf("<B>Gene%s %s ID:</B> " "<A HREF=\"http://flybase.net/reports/%s.html\" " "TARGET=_BLANK>%s</A><BR>\n", gNum, idType, fbgnId, psc->geneIds[i]); } } pscreenFree(&psc); } else errAbort("query returned no results: \"%s\"", query); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } static void doOligoMatch(char *item) /* Print info about oligo match. */ { char *oligo = cartUsualString(cart, oligoMatchVar, cloneString(oligoMatchDefault)); touppers(oligo); cartWebStart(cart, database, "Perfect Matches to Short Sequence"); printf("<B>Sequence:</B> %s<BR>\n", oligo); printf("<B>Chromosome:</B> %s<BR>\n", seqName); printf("<B>Start:</B> %s<BR>\n", item+1); printf("<B>Strand:</B> %c<BR>\n", item[0]); webIncludeHelpFile(OLIGO_MATCH_TRACK_NAME, TRUE); } struct slName *cutterIsoligamers(struct cutter *myEnzyme) /* Find enzymes with same cut site. */ { struct sqlConnection *conn; struct cutter *cutters = NULL; struct slName *ret = NULL; conn = hAllocConn("hgFixed"); cutters = cutterLoadByQuery(conn, NOSQLINJ "select * from cutters"); ret = findIsoligamers(myEnzyme, cutters); hFreeConn(&conn); cutterFreeList(&cutters); return ret; } void cutterPrintSite(struct cutter *enz) /* Print out the enzyme REBASE style. */ { int i; for (i = 0; i < enz->size+1; i++) { if (i == enz->cut) printf("^"); else if (i == enz->cut + enz->overhang) printf("v"); if (i < enz->size) printf("%c", enz->seq[i]); } } static void doCuttersEnzymeList(struct sqlConnection *conn, char *getBed, char *c, char *l, char *r) /* Print out list of enzymes (BED). This function will exit the program. */ { struct cutter *cut = NULL; char query[100]; struct dnaSeq *winDna; struct bed *bedList = NULL, *oneBed; int s, e; if (!c || !l || !r) errAbort("Bad Range"); s = atoi(l); e = atoi(r); winDna = hDnaFromSeq(database, c, s, e, dnaUpper); if (sameString(getBed, "all")) sqlSafef(query, sizeof(query), "select * from cutters"); else sqlSafef(query, sizeof(query), "select * from cutters where name=\'%s\'", getBed); cut = cutterLoadByQuery(conn, query); bedList = matchEnzymes(cut, winDna, s); printf("<HTML>\n<HEAD>\n%s<TITLE>Enzyme Output</TITLE></HEAD>\n<BODY><PRE><TT>", getCspMetaHeader()); for (oneBed = bedList; oneBed != NULL; oneBed = oneBed->next) { freeMem(oneBed->chrom); oneBed->chrom = cloneString(c); bedTabOutN(oneBed, 6, stdout); } puts("</TT></PRE>\n"); cartFooter(); bedFreeList(&bedList); cutterFreeList(&cut); hFreeConn(&conn); exit(0); } static void doCutters(char *item) /* Print info about a restriction enzyme. */ { struct sqlConnection *conn; struct cutter *cut = NULL; char query[100]; char *doGetBed = cgiOptionalString("doGetBed"); char *c = cgiOptionalString("c"); char *l = cgiOptionalString("l"); char *r = cgiOptionalString("r"); conn = hAllocConn("hgFixed"); if (doGetBed) doCuttersEnzymeList(conn, doGetBed, c, l, r); sqlSafef(query, sizeof(query), "select * from cutters where name=\'%s\'", item); cut = cutterLoadByQuery(conn, query); cartWebStart(cart, database, "Restriction Enzymes from REBASE"); if (cut) { char *o = cgiOptionalString("o"); char *t = cgiOptionalString("t"); struct slName *isoligs = cutterIsoligamers(cut); printf("<B>Enzyme Name:</B> %s<BR>\n", cut->name); /* Display position only if click came from hgTracks. */ if (c && o && t) { int left = atoi(o); int right = atoi(t); printPosOnChrom(c, left, right, NULL, FALSE, cut->name); } puts("<B>Recognition Sequence: </B>"); cutterPrintSite(cut); puts("<BR>\n"); printf("<B>Palindromic: </B>%s<BR>\n", (cut->palindromic) ? "YES" : "NO"); if (cut->numSciz > 0) { int i; puts("<B>Isoschizomers: </B>"); for (i = 0; i < cut->numSciz-1; i++) printf("<A HREF=\"%s&g=%s&i=%s\">%s</A>, ", hgcPathAndSettings(), CUTTERS_TRACK_NAME, cut->scizs[i], cut->scizs[i]); printf("<A HREF=\"%s&g=%s&i=%s\">%s</A><BR>\n", hgcPathAndSettings(), CUTTERS_TRACK_NAME, cut->scizs[cut->numSciz-1], cut->scizs[cut->numSciz-1]); } if (isoligs) { struct slName *cur; puts("<B>Isoligamers: </B>"); for (cur = isoligs; cur->next != NULL; cur = cur->next) printf("<A HREF=\"%s&g=%s&i=%s\">%s</A>, ", hgcPathAndSettings(), CUTTERS_TRACK_NAME, cur->name, cur->name); printf("<A HREF=\"%s&g=%s&i=%s\">%s</A><BR>\n", hgcPathAndSettings(), CUTTERS_TRACK_NAME, cur->name, cur->name); slFreeList(&isoligs); } if (cut->numRefs > 0) { int i, count = 1; char **row; struct sqlResult *sr; puts("<B>References:</B><BR>\n"); sqlSafef(query, sizeof(query), "select * from rebaseRefs"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { int refNum = atoi(row[0]); for (i = 0; i < cut->numRefs; i++) { if (refNum == cut->refs[i]) printf("%d. %s<BR>\n", count++, row[1]); } } sqlFreeResult(&sr); } if (c && o && t) { puts("<BR><B>Download BED of enzymes in this browser range:</B> "); printf("<A HREF=\"%s&g=%s&l=%s&r=%s&c=%s&doGetBed=all\">all enzymes</A>, ", hgcPathAndSettings(), CUTTERS_TRACK_NAME, l, r, c); printf("<A HREF=\"%s&g=%s&l=%s&r=%s&c=%s&doGetBed=%s\">just %s</A><BR>\n", hgcPathAndSettings(), CUTTERS_TRACK_NAME, l, r, c, cut->name, cut->name); } } webIncludeHelpFile(CUTTERS_TRACK_NAME, TRUE); cutterFree(&cut); hFreeConn(&conn); } static void doAnoEstTcl(struct trackDb *tdb, char *item) /* Print info about AnoEst uniquely-clustered item. */ { struct sqlConnection *conn = hAllocConn(database); int start = cartInt(cart, "o"); genericHeader(tdb, item); printCustomUrl(tdb, item, TRUE); genericBedClick(conn, tdb, item, start, 12); if (hTableExists(database, "anoEstExpressed")) { char query[512]; sqlSafef(query, sizeof(query), "select 1 from anoEstExpressed where name = '%s'", item); if (sqlQuickNum(conn, query)) puts("<B>Expressed:</B> yes<BR>"); else puts("<B>Expressed:</B> no<BR>"); } hFreeConn(&conn); printTrackHtml(tdb); } void mammalPsgTableRow(char *test, char *description, float pVal, unsigned isFdrSignificant) /* print single row of the overview table for mammal PSG track */ { char *start = ""; char *end = ""; if (isFdrSignificant) { start = "<b>"; end = "</b>"; } if (pVal<=1) { printf("<tr><td>%s%s%s</td><td>%s%s%s</td><td>%s%.02g%s</tr>\n", start,test,end, start,description,end, start,pVal,end); } } void doMammalPsg(struct trackDb *tdb, char *itemName) /* create details page for mammalPsg track */ { struct mammalPsg *mammalPsg = NULL; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char *bayesianFiguresUrl = "../images/mammalPsg"; genericHeader(tdb, itemName); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) mammalPsg = mammalPsgLoad(row); else errAbort("Can't find item '%s'", itemName); sqlFreeResult(&sr); /* first print the same thing that you would print for ordinary bed track */ bedPrintPos((struct bed *) mammalPsg,12,tdb); /* rows showing the results of individual likelihood ratio tests */ printf("<p><b>Likelihood ratio tests for positive selection:</b></p>\n"); printf("<p><table border=1>\n"); printf("<tr><th>Test</th><th>Description</th><th>P-value</th>"); mammalPsgTableRow("A","all branches",mammalPsg->lrtAllPValue,mammalPsg->lrtAllIsFdr); mammalPsgTableRow("B","branch leading to primates",mammalPsg->lrtPrimateBrPValue,mammalPsg->lrtPrimateBrIsFdr); mammalPsgTableRow("C","primate clade",mammalPsg->lrtPrimateClPValue,mammalPsg->lrtPrimateClIsFdr); mammalPsgTableRow("D","branch leading to rodents",mammalPsg->lrtRodentBrPValue,mammalPsg->lrtRodentBrIsFdr); mammalPsgTableRow("E","rodent clade",mammalPsg->lrtRodentClPValue,mammalPsg->lrtRodentClIsFdr); mammalPsgTableRow("F","human branch",mammalPsg->lrtHumanPValue,mammalPsg->lrtHumanIsFdr); mammalPsgTableRow("G","chimp branch",mammalPsg->lrtChimpPValue,mammalPsg->lrtChimpIsFdr); mammalPsgTableRow("H","branch leading to hominids",mammalPsg->lrtHominidPValue,mammalPsg->lrtHominidIsFdr); mammalPsgTableRow("I","macaque branch",mammalPsg->lrtMacaquePValue,mammalPsg->lrtMacaqueIsFdr); printf("</table></p>\n"); printf("<p>(FDR significant P-value shown in boldface)</p>\n"); /* pictures showing the Bayesian analysis */ if (mammalPsg->bestHist > 0) { printf("<p><b>Results of Bayesian analysis:</b><br>\n"); printf("<table border=0 cellpadding=20><tr>\n"); printf("<td align=center><b>Best model - posterior prob. %.2f</b><br> <br><img src=\"%s/model-%d-1.jpg\"></td>\n", mammalPsg->bestHistPP,bayesianFiguresUrl,mammalPsg->bestHist); printf("<td align=center><b>2nd best - posterior prob. %.2f</b><br> <br><img src=\"%s/model-%d-1.jpg\"></td>\n", mammalPsg->nextBestHistPP,bayesianFiguresUrl,mammalPsg->nextBestHist); printf("</tr></table></p>\n"); } printTrackHtml(tdb); hFreeConn(&conn); } void doDless(struct trackDb *tdb, char *itemName) /* create details page for DLESS */ { struct dless *dless = NULL; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; boolean approx; enum {CONS, GAIN, LOSS} elementType; genericHeader(tdb, itemName); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) dless = dlessLoad(row); else errAbort("Can't find item '%s'", itemName); sqlFreeResult(&sr); approx = sameString(dless->condApprox, "approx"); if (sameString(dless->type, "conserved")) elementType = CONS; else if (sameString(dless->type, "gain")) elementType = GAIN; else elementType = LOSS; if (elementType == CONS) printf("<B>Prediction:</B> conserved in all species<BR>\n"); else printf("<B>Prediction:</B> %s of element on branch above node labeled \"%s\"<BR>\n", elementType == GAIN ? "gain" : "loss", dless->branch); printPos(dless->chrom, dless->chromStart, dless->chromEnd, NULL, FALSE, dless->name); printf("<B>Log-odds score:</B> %.1f bits<BR>\n", dless->score); if (elementType == CONS) { printf("<B>P-value of conservation:</B> %.2e<BR><BR>\n", dless->pConsSub); printf("<B>Numbers of substitutions:</B>\n<UL>\n"); printf("<LI>Null distribution: mean = %.2f, var = %.2f, 95%% c.i. = [%d, %d]\n", dless->priorMeanSub, dless->priorVarSub, dless->priorMinSub, dless->priorMaxSub); printf("<LI>Posterior distribution: mean = %.2f, var = %.2f\n</UL>\n", dless->postMeanSub, dless->postVarSub); } else { printf("<B>P-value of conservation in subtree:</B> %.2e<BR>\n", dless->pConsSub); printf("<B>P-value of conservation in rest of tree:</B> %.2e<BR>\n", dless->pConsSup); printf("<B>P-value of conservation in subtree given total:</B> %.2e%s<BR>\n", dless->pConsSubCond, approx ? "*" : ""); printf("<B>P-value of conservation in rest of tree given total:</B> %.2e%s<BR><BR>\n", dless->pConsSupCond, approx ? "*" : ""); printf("<B>Numbers of substitutions in subtree beneath event</B>:\n<UL>\n"); printf("<LI>Null distribution: mean = %.2f, var = %.2f, 95%% c.i. = [%d, %d]\n", dless->priorMeanSub, dless->priorVarSub, dless->priorMinSub, dless->priorMaxSub); printf("<LI>Posterior distribution: mean = %.2f, var = %.2f\n", dless->postMeanSub, dless->postVarSub); printf("</UL><B>Numbers of substitutions in rest of tree:</B>\n<UL>\n"); printf("<LI>Null distribution: mean = %.2f, var = %.2f, 95%% c.i. = [%d, %d]\n", dless->priorMeanSup, dless->priorVarSup, dless->priorMinSup, dless->priorMaxSup); printf("<LI>Posterior distribution: mean = %.2f, var = %.2f\n</UL>\n", dless->postMeanSup, dless->postVarSup); if (approx) printf("* = Approximate p-value (usually conservative)<BR>\n"); } printTrackHtml(tdb); hFreeConn(&conn); } void showSomeAlignment2(struct psl *psl, bioSeq *qSeq, enum gfType qType, int qStart, int qEnd, char *entryName, char *geneName, char *geneTable, int cdsS, int cdsE) /* Display protein or DNA alignment in a frame. */ { int blockCount = 0, i = 0, j= 0, *exnStarts = NULL, *exnEnds = NULL; struct tempName indexTn, bodyTn; FILE *index, *body; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; struct genePred *gene = NULL; char **row, query[256]; int tStart = psl->tStart; int tEnd = psl->tEnd; char tName[256]; struct dnaSeq *tSeq; char *tables[4] = {"luGene", "refGene", "mgcGenes", "luGene2"}; /* open file to write to */ trashDirFile(&indexTn, "index", "index", ".html"); trashDirFile(&bodyTn, "body", "body", ".html"); body = mustOpen(bodyTn.forCgi, "w"); /* get query genes struct info*/ for(i = 0; i < 4; i++) { if(sqlTableExists(conn, tables[i])) { sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s'" "AND chrom = '%s' AND txStart <= %d " "AND txEnd >= %d", tables[i], geneName, psl->qName, qStart, qEnd); sr = sqlMustGetResult(conn, query); if((row = sqlNextRow(sr)) != NULL) { int hasBin = 0; if(hOffsetPastBin(database, psl->qName, tables[i])) hasBin=1; gene = genePredLoad(row+hasBin); break; } else sqlFreeResult(&sr); } } if(i == 4) errAbort("Can't find query for %s in %s. This entry may no longer exist\n", geneName, geneTable); AllocArray(exnStarts, gene->exonCount); AllocArray(exnEnds, gene->exonCount); for(i = 0; i < gene->exonCount; i++) { if(gene->exonStarts[i] < qEnd && gene->exonEnds[i] > qStart) { exnStarts[j] = gene->exonStarts[i] > qStart ? gene->exonStarts[i] : qStart; exnEnds[j] = gene->exonEnds[i] < qEnd ? gene->exonEnds[i] : qEnd; j++; } } genePredFree(&gene); /* Writing body of alignment. */ body = mustOpen(bodyTn.forCgi, "w"); htmStartDirDepth(body, psl->qName, 2); /* protein psl's have a tEnd that isn't quite right */ if ((psl->strand[1] == '+') && (qType == gftProt)) tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1] * 3; tSeq = hDnaFromSeq(database, seqName, psl->tStart, psl->tEnd, dnaLower); freez(&tSeq->name); tSeq->name = cloneString(psl->tName); safef(tName, sizeof(tName), "%s.%s", organism, psl->tName); if (psl->qName == NULL) fprintf(body, "<H2>Alignment of %s and %s:%d-%d</H2>\n", entryName, psl->tName, psl->tStart+1, psl->tEnd); else fprintf(body, "<H2>Alignment of %s and %s:%d-%d</H2>\n", entryName, psl->tName, psl->tStart+1, psl->tEnd); fputs("Click on links in the frame to the left to navigate through " "the alignment.\n", body); safef(tName, sizeof(tName), "%s.%s", organism, psl->tName); blockCount = pslGenoShowAlignment(psl, qType == gftProt, entryName, qSeq, qStart, qEnd, tName, tSeq, tStart, tEnd, exnStarts, exnEnds, j, body); freez(&exnStarts); freez(&exnEnds); freeDnaSeq(&tSeq); htmEnd(body); fclose(body); chmod(bodyTn.forCgi, 0666); /* Write index. */ index = mustOpen(indexTn.forCgi, "w"); if (entryName == NULL) entryName = psl->qName; htmStartDirDepth(index, entryName, 2); fprintf(index, "<H3>Alignment of %s</H3>", entryName); fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, entryName); fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), psl->tName); for (i=1; i<=blockCount; ++i) { fprintf(index, "<A HREF=\"../%s#%d\" TARGET=\"body\">block%d</A><BR>\n", bodyTn.forCgi, i, i); } fprintf(index, "<A HREF=\"../%s#ali\" TARGET=\"body\">together</A><BR>\n", bodyTn.forCgi); htmEnd(index); fclose(index); chmod(indexTn.forCgi, 0666); /* Write (to stdout) the main html page containing just the frame info. */ puts("<FRAMESET COLS = \"13%,87% \" >"); printf(" <FRAME SRC=\"%s\" NAME=\"index\">\n", indexTn.forCgi); printf(" <FRAME SRC=\"%s\" NAME=\"body\">\n", bodyTn.forCgi); puts("<NOFRAMES><BODY></BODY></NOFRAMES>"); puts("</FRAMESET>"); puts("</HTML>\n"); exit(0); /* Avoid cartHtmlEnd. */ } void potentPslAlign(char *htcCommand, char *item) {/* show the detail psl alignment between genome */ char *pslTable = cgiString("pslTable"); char *chrom = cgiString("chrom"); int start = cgiInt("cStart"); int end = cgiInt("cEnd"); struct psl *psl = NULL; struct dnaSeq *qSeq = NULL; char *db = cgiString("db"); char name[64]; char query[256], fullTable[HDB_MAX_TABLE_STRING]; char **row; boolean hasBin; struct sqlResult *sr = NULL; struct sqlConnection *conn = hAllocConn(database); if (!hFindSplitTable(database, seqName, pslTable, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", pslTable); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE " "tName = '%s' AND tStart = %d " "AND tEnd = %d", pslTable, chrom, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if(row != NULL) { psl = pslLoad(row+hasBin); } else { errAbort("No alignment infomation\n"); } qSeq = loadGenomePart(db, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s in %s(%d-%d)", item,psl->qName, psl->qStart, psl->qEnd); char title[1024]; safef(title, sizeof title, "%s %dk", name, psl->qStart/1000); htmlFramesetStart(title); showSomeAlignment2(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, item, "", psl->qStart, psl->qEnd); } void doPutaFrag(struct trackDb *tdb, char *item) /* display the potential pseudo and coding track */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row, table[256], query[256], *parts[6]; struct putaInfo *info = NULL; int start = cartInt(cart, "o"), end = cartInt(cart, "t"); char *db = cgiString("db"); char *name = cartString(cart, "i"), *chr = cartString(cart, "c"); char pslTable[256]; char otherString[256]; safef(table, sizeof table, "putaInfo"); safef(pslTable, sizeof pslTable, "potentPsl"); cartWebStart(cart, database, "Putative Coding or Pseudo Fragments"); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", table, name, chr, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if(row != NULL) { info = putaInfoLoad(row+1); } else { errAbort("Can't find information for %s in data base\n", name); } sqlFreeResult(&sr); char *tempName = cloneString(name); chopByChar(tempName, '|',parts, 4); printf("<B>%s</B> is homologous to the known gene: <A HREF=\"", name); printEntrezNucleotideUrl(stdout, parts[0]); printf("\" TARGET=_blank>%s</A><BR>\n", parts[0]); printf("<B>%s </B>is aligned here with score : %d<BR><BR>\n", parts[0], info->score); /* print the info about the stamper gene */ printf("<B> %s</B><BR>\n", parts[0]); printf("<B>Genomic location of the mapped part of %s</B>: <A HREF=\"" "%s?db=%s&position=%s:%d-%d\" TARGET=_blank>%s(%s):%d-%d </A> <BR>\n", parts[0], hgTracksName(), db, info->oChrom, info->oChromStart, info->oChromEnd, info->oChrom, parts[2],info->oChromStart+1, info->oChromEnd); printf("<B>Mapped %s Exons</B>: %d of %d. <BR> <B>Mapped %s CDS exons</B>: %d of %d <BR>\n", parts[0], info->qExons[0], info->qExons[1], parts[0], info->qExons[2], info->qExons[3]); printf("<b>Aligned %s bases</B>:%d of %d with %f identity. <BR> <B>Aligned %s CDS bases</B>: %d of %d with %f identity.<BR><BR>\n", parts[0],info->qBases[0], info->qBases[1], info->id[0], parts[0], info->qBases[2], info->qBases[3], info->id[1]); /* print info about the stamp putative element */ printf("<B>%s </B><BR> <B>Genomic location: </B>" " <A HREF=\"%s?db=%s&position=%s:%d-%d\" >%s(%s): %d - %d</A> <BR> <B> Element Structure: </B> %d putative exons and %d putative cds exons<BR><BR>\n", name, hgTracksName(), db, info->chrom, info->chromStart+1, info->chromEnd, info->chrom, info->strand, info->chromStart+1, info->chromEnd, info->tExons[0], info->tExons[1]); if(info->repeats[0] > 0) { printf("Repeats elements inserted into %s <BR>\n", name); } if(info->stop >0) { int k = 0; printf("Premature stops in block "); for(k = 0; k < info->blockCount; k++) { if(info->stops[k] > 0) { if(info->strand[0] == '+') printf("%d ",k+1); else printf("%d ", info->blockCount - k); } } printf("<BR>\n"); } /* show genome sequence */ hgcAnchorSomewhere("htcGeneInGenome", info->name, tdb->track, seqName); printf("View DNA for this putative fragment</A><BR>\n"); /* show the detail alignment */ sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE " "tName = '%s' AND tStart = %d " "AND tEnd = %d AND strand = '%c%c'", pslTable, info->chrom, info->chromStart, info->chromEnd, parts[2][0], info->strand[0]); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if(row != NULL) { safef(otherString, sizeof otherString, "&db=%s&pslTable=%s&chrom=%s&cStart=%d&cEnd=%d&strand=%s&qStrand=%s", database, pslTable, info->chrom,info->chromStart, info->chromEnd, info->strand, parts[2]); hgcAnchorSomewhere("potentPsl", parts[0], otherString, info->chrom); printf("<BR>View details of parts of alignment </A>.</BR>\n"); } sqlFreeResult(&sr); putaInfoFree(&info); hFreeConn(&conn); } void doInterPro(struct trackDb *tdb, char *itemName) { char condStr[255]; char *desc; struct sqlConnection *conn; genericHeader(tdb, itemName); conn = hAllocConn(database); sqlSafefFrag(condStr, sizeof condStr, "interProId='%s'", itemName); desc = sqlGetField("proteome", "interProXref", "description", condStr); printf("<B>Item:</B> %s <BR>\n", itemName); printf("<B>Description:</B> %s <BR>\n", desc); printf("<B>Outside Link:</B> "); printf("<A HREF="); printf("http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=%s", itemName); printf(" Target=_blank> %s </A> <BR>\n", itemName); printTrackHtml(tdb); hFreeConn(&conn); } void doDv(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct dvBed dvBed; struct dv *dv; struct dvXref2 *dvXref2; struct omimTitle *omimTitle; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr, *sr2, *sr3, *sr4; char **row; char query[256], query2[256], query3[256], query4[256]; int rowOffset = hOffsetPastBin(database, seqName, table); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); printf("<B>Item:</B> %s <BR>\n", itemName); printf("<B>Outside Link:</B> "); printf("<A HREF="); printSwissProtVariationUrl(stdout, itemName); printf(" Target=_blank> %s </A> <BR>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { dvBedStaticLoad(row+rowOffset, &dvBed); bedPrintPos((struct bed *)&dvBed, 3, tdb); } sqlFreeResult(&sr); sqlSafef(query2, sizeof(query2), "select * from dv where varId = '%s' ", itemName); sr2 = sqlGetResult(conn, query2); while ((row = sqlNextRow(sr2)) != NULL) { /* not using static load */ dv = dvLoad(row); printf("<B>Swiss-prot ID:</B> %s <BR>\n", dv->spID); printf("<B>Start:</B> %d <BR>\n", dv->start); printf("<B>Length:</B> %d <BR>\n", dv->len); printf("<B>Original:</B> %s <BR>\n", dv->orig); printf("<B>Variant:</B> %s <BR>\n", dv->variant); dvFree(&dv); } sqlFreeResult(&sr2); sqlSafef(query3, sizeof(query3), "select * from dvXref2 where varId = '%s' ", itemName); char *protDbName = hPdbFromGdb(database); struct sqlConnection *protDbConn = hAllocConn(protDbName); sr3 = sqlGetResult(protDbConn, query3); while ((row = sqlNextRow(sr3)) != NULL) { dvXref2 = dvXref2Load(row); if (sameString("MIM", dvXref2->extSrc)) { printf("<B>OMIM:</B> "); printf("<A HREF="); printOmimUrl(stdout, dvXref2->extAcc); printf(" Target=_blank> %s</A> \n", dvXref2->extAcc); /* nested query here */ if (hTableExists(database, "omimTitle")) { sqlSafef(query4, sizeof(query4), "select * from omimTitle where omimId = '%s' ", dvXref2->extAcc); sr4 = sqlGetResult(conn, query4); while ((row = sqlNextRow(sr4)) != NULL) { omimTitle = omimTitleLoad(row); printf("%s\n", omimTitle->title); omimTitleFree(&omimTitle); } } printf("<BR>\n"); } dvXref2Free(&dvXref2); } sqlFreeResult(&sr3); hFreeConn(&protDbConn); printTrackHtml(tdb); hFreeConn(&conn); } void printOregannoLink (struct oregannoLink *link) /* this prints a link for oreganno */ { struct hash *linkInstructions = NULL; struct hash *thisLink = NULL; char *linktype, *label = NULL; hgReadRa(database, organism, rootDir, "links.ra", &linkInstructions); /* determine how to do link from .ra file */ thisLink = hashFindVal(linkInstructions, link->raKey); if (thisLink == NULL) return; /* no link found */ /* type determined by fields eg url */ linktype = hashFindVal(thisLink, "url"); label = hashFindVal(thisLink, "label"); if (linktype != NULL) { char url[256]; char *accFlag = hashFindVal(thisLink, "acc"); if (accFlag == NULL) safecpy(url, sizeof(url), linktype); else { char *accNum = hashFindVal(thisLink, "accNum"); if (accNum == NULL) safef(url, sizeof(url), linktype, link->attrAcc); else if (sameString(accNum, "2")) { char *val[2]; char *copy = cloneString(link->attrAcc); if (2 == chopString(copy, ",", val, 2)) safef(url, sizeof(url), linktype, val[0], val[1]); } } if (label == NULL) label = ""; /* no label */ printf("%s - <A HREF=\"%s\" TARGET=\"_BLANK\">%s</A>\n", label, url, link->attrAcc); } } void doOreganno(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct oreganno *r = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *prevLabel = NULL; int i = 0, listStarted = 0; //int start = cartInt(cart, "o"); genericHeader(tdb, itemName); /* postion, band, genomic size */ sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { r = oregannoLoad(row); printf("<B>ORegAnno ID:</B> %s <BR>\n", r->id); #if 0 // all the same as the ID for now printf("<B>ORegAnno name:</B> %s <BR>\n", r->name); #endif printf("<B>Strand:</B> %s<BR>\n", r->strand); bedPrintPos((struct bed *)r, 3, tdb); /* start html list for attributes */ printf("<DL>"); } sqlFreeResult(&sr); if (sameString(table, "oregannoOther")) { printf("<B>Attributes as described from other species</B><BR>\n"); } /* fetch and print the attributes */ for (i=0; i < oregannoAttrSize; i++) { int used = 0; char *tab; if (sameString(table, "oregannoOther")) tab = cloneString("oregannoOtherAttr"); else tab = cloneString("oregannoAttr"); /* names are quote safe, come from oregannoUi.c */ sqlSafef(query, sizeof(query), "select * from %s where id = '%s' and attribute = '%s'", tab, r->id, oregannoAttributes[i]); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct oregannoAttr attr; used++; if (used == 1) { if (!prevLabel || differentString(prevLabel, oregannoAttrLabel[i])) { if (listStarted == 0) listStarted = 1; else printf("</DD>"); printf("<DT><b>%s:</b></DT><DD>\n", oregannoAttrLabel[i]); freeMem(prevLabel); prevLabel = cloneString(oregannoAttrLabel[i]); } } oregannoAttrStaticLoad(row, &attr); printf("%s ", attr.attrVal); printf("<BR>\n"); } freeMem(tab); if (sameString(table, "oregannoOther")) tab = cloneString("oregannoOtherLink"); else tab = cloneString("oregannoLink"); sqlSafef(query, sizeof(query), "select * from %s where id = '%s' and attribute = '%s'", tab, r->id, oregannoAttributes[i]); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct oregannoLink link; used++; if (used == 1) { if (!prevLabel || differentString(prevLabel, oregannoAttrLabel[i])) { if (listStarted == 0) listStarted = 1; else printf("</DD>"); printf("<DT><b>%s:</b></DT><DD>\n", oregannoAttrLabel[i]); freeMem(prevLabel); prevLabel = cloneString(oregannoAttrLabel[i]); } } oregannoLinkStaticLoad(row, &link); printOregannoLink(&link); printf("<BR>\n"); } freeMem(tab); } if (listStarted > 0) printf("</DD></DL>"); oregannoFree(&r); freeMem(prevLabel); printTrackHtml(tdb); hFreeConn(&conn); } void doSnpArray (struct trackDb *tdb, char *itemName, char *dataSource) { char *table = tdb->table; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); int end = 0; // char *chrom = cartString(cart, "c"); char nibName[HDB_MAX_PATH_STRING]; struct dnaSeq *seq; genericHeader(tdb, itemName); /* Affy uses their own identifiers */ if (sameString(dataSource, "Affy")) sqlSafef(query, sizeof(query), "select chromEnd, strand, observed, rsId from %s where chrom = '%s' and chromStart=%d", table, seqName, start); else sqlSafef(query, sizeof(query), "select chromEnd, strand, observed from %s where chrom = '%s' and chromStart=%d", table, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { end = sqlUnsigned(row[0]); printPosOnChrom(seqName, start, end, row[1], FALSE, NULL); printf("<B>Polymorphism:</B> %s \n", row[2]); if (end == start + 1) { hNibForChrom(database, seqName, nibName); seq = hFetchSeq(nibName, seqName, start, end); touppers(seq->dna); if (sameString(row[1], "-")) reverseComplement(seq->dna, 1); printf("<BR><B>Reference allele:</B> %s \n", seq->dna); } if (sameString(dataSource, "Affy")) { printf("<BR><BR><A HREF=\"https://www.affymetrix.com/LinkServlet?probeset=%s\" TARGET=_blank>NetAffx</A> (log in required, registration is free)\n", itemName); if (regexMatch(row[3], "^rs[0-9]+$")) { printf("<BR>"); printDbSnpRsUrl(row[3], "dbSNP (%s)", row[3]); } } else if (regexMatch(itemName, "^rs[0-9]+$")) { printf("<BR>"); printDbSnpRsUrl(itemName, "dbSNP (%s)", itemName); } } sqlFreeResult(&sr); printTrackHtml(tdb); hFreeConn(&conn); } void doSnpArray2 (struct trackDb *tdb, char *itemName, char *dataSource) /* doSnpArray2 is essential the same as doSnpArray except that the strand is blanked out */ /* This is a temp solution for 3 Illumina SNP Arrays to blank out strand info for non-dbSnp entries */ /* Should be removed once Illumina comes up with a clear defintion of their strand data */ { char *table = tdb->table; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); int end = 0; char nibName[HDB_MAX_PATH_STRING]; struct dnaSeq *seq; genericHeader(tdb, itemName); /* Affy uses their own identifiers */ if (sameString(dataSource, "Affy")) sqlSafef(query, sizeof(query), "select chromEnd, strand, observed, rsId from %s where chrom = '%s' and chromStart=%d", table, seqName, start); else sqlSafef(query, sizeof(query), "select chromEnd, strand, observed from %s where chrom = '%s' and chromStart=%d", table, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { end = sqlUnsigned(row[0]); /* force strand info to be blank for non-dbSnp entries, per Illumina's request */ printPosOnChrom(seqName, start, end, " ", FALSE, NULL); printf("<B>Polymorphism:</B> %s \n", row[2]); if (end == start + 1) { hNibForChrom(database, seqName, nibName); seq = hFetchSeq(nibName, seqName, start, end); touppers(seq->dna); if (sameString(row[1], "-")) reverseComplement(seq->dna, 1); printf("<BR><B>Reference allele:</B> %s \n", seq->dna); } if (sameString(dataSource, "Affy")) { printf("<BR><BR><A HREF=\"https://www.affymetrix.com/LinkServlet?probeset=%s\" TARGET=_blank>NetAffx</A> (log in required, registration is free)\n", itemName); if (regexMatch(row[3], "^rs[0-9]+$")) { printf("<BR>"); printDbSnpRsUrl(row[3], "dbSNP (%s)", row[3]); } } else if (regexMatch(itemName, "^rs[0-9]+$")) { printf("<BR>"); printDbSnpRsUrl(itemName, "dbSNP (%s)", itemName); } } sqlFreeResult(&sr); printTrackHtml(tdb); hFreeConn(&conn); } void printGvAttrCatType (int i) /* prints new category and type labels for attributes as needed */ { /* only print name and category if different */ if (gvPrevCat == NULL) { /* print start of both */ /* if need to print category layer, here is where print first */ printf("<DT><B>%s:</B></DT><DD>\n", gvAttrTypeDisplay[i]); gvPrevCat = cloneString(gvAttrCategory[i]); gvPrevType = cloneString(gvAttrTypeDisplay[i]); } else if (differentString(gvPrevCat, gvAttrCategory[i])) { /* end last, and print start of both */ printf("</DD>"); /* if/when add category here is where to print next */ printf("<DT><B>%s:</B></DT><DD>\n", gvAttrTypeDisplay[i]); freeMem(gvPrevType); gvPrevType = cloneString(gvAttrTypeDisplay[i]); freeMem(gvPrevCat); gvPrevCat = cloneString(gvAttrCategory[i]); } else if (sameString(gvPrevCat, gvAttrCategory[i]) && differentString(gvPrevType, gvAttrTypeDisplay[i])) { /* print new name */ printf("</DD>"); printf("<DT><B>%s:</B></DT><DD>\n", gvAttrTypeDisplay[i]); freeMem(gvPrevType); gvPrevType = cloneString(gvAttrTypeDisplay[i]); } /* else don't need type or category */ } void printLinksRaLink (char *acc, char *raKey, char *displayVal) /* print a link with instructions in hgcData/links.ra file */ { struct hash *linkInstructions = NULL; struct hash *thisLink = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *linktype, *label; char *doubleEntry = NULL; hgReadRa(database, organism, rootDir, "links.ra", &linkInstructions); /* determine how to do link from .ra file */ thisLink = hashFindVal(linkInstructions, raKey); if (thisLink == NULL) return; /* no link found */ /* type determined by fields: url = external, dataSql = internal, others added later? */ /* need to print header here for some displays */ linktype = hashFindVal(thisLink, "dataSql"); label = hashFindVal(thisLink, "label"); if (label == NULL) label = ""; if (linktype != NULL) { sqlSafef(query, sizeof(query), linktype, acc); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { /* should this print more than 1 column, get count from ra? */ if (row[0] != NULL) { /* print label and result */ printf("<B>%s</B> - %s", label, row[0]); /* check for link */ doubleEntry = hashFindVal(thisLink, "dataLink"); if (doubleEntry != NULL) { char url[512]; struct hash *newLink; char *accCol = NULL, *format = NULL; int colNum = 1; newLink = hashFindVal(linkInstructions, doubleEntry); accCol = hashFindVal(thisLink, "dataLinkCol"); if (newLink == NULL || accCol == NULL) errAbort("missing required fields in .ra file"); colNum = atoi(accCol); format = hashFindVal(newLink, "url"); safef(url, sizeof(url), format, row[colNum - 1]); printf(" - <A HREF=\"%s\" TARGET=_blank>%s</A>\n", url, row[colNum - 1]); } printf("<BR>\n"); } } sqlFreeResult(&sr); } else { linktype = hashFindVal(thisLink, "url"); if (linktype != NULL) { char url[512]; char *encodedAcc = cgiEncode(acc); char *encode = hashFindVal(thisLink, "needsEncoded"); if (encode != NULL && sameString(encode, "yes")) safef(url, sizeof(url), linktype, encodedAcc); else safef(url, sizeof(url), linktype, acc); if (displayVal == NULL || sameString(displayVal, "")) printf("<B>%s</B> - <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", label, url, acc); else printf("<B>%s</B> - <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", label, url, displayVal); } } hFreeConn(&conn); return; } int printProtVarLink (char *id, int i) { struct protVarLink *link = NULL; struct hash *linkInstructions = NULL; struct hash *thisLink = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *linktype, *label; char *doubleEntry = NULL; int attrCnt = 0; hgReadRa(database, organism, rootDir, "links.ra", &linkInstructions); sqlSafef(query, sizeof(query), "select * from protVarLink where id = '%s' and attrType = '%s'", id, gvAttrTypeKey[i]); /* attrType == gvAttrTypeKey should be quote safe */ sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct sqlResult *sr2; char **row2; attrCnt++; link = protVarLinkLoad(row); /* determine how to do link from .ra file */ thisLink = hashFindVal(linkInstructions, link->raKey); if (thisLink == NULL) continue; /* no link found */ /* type determined by fields: url = external, dataSql = internal, others added later? */ printGvAttrCatType(i); /* only print header if data */ linktype = hashFindVal(thisLink, "dataSql"); label = hashFindVal(thisLink, "label"); if (label == NULL) label = ""; if (linktype != NULL) { sqlSafef(query, sizeof(query), linktype, link->acc); sr2 = sqlGetResult(conn2, query); while ((row2 = sqlNextRow(sr2)) != NULL) { /* should this print more than 1 column, get count from ra? */ if (row2[0] != NULL) { /* print label and result */ printf("<B>%s</B> - %s", label, row2[0]); /* check for link */ doubleEntry = hashFindVal(thisLink, "dataLink"); if (doubleEntry != NULL) { char url[512]; struct hash *newLink; char *accCol = NULL, *format = NULL; int colNum = 1; newLink = hashFindVal(linkInstructions, doubleEntry); accCol = hashFindVal(thisLink, "dataLinkCol"); if (newLink == NULL || accCol == NULL) errAbort("missing required fields in .ra file"); colNum = atoi(accCol); format = hashFindVal(newLink, "url"); safef(url, sizeof(url), format, row2[colNum - 1]); printf(" - <A HREF=\"%s\" TARGET=_blank>%s</A>\n", url, row2[colNum - 1]); } printf("<BR>\n"); } } sqlFreeResult(&sr2); } else { linktype = hashFindVal(thisLink, "url"); if (linktype != NULL) { char url[1024]; char *encodedAcc = cgiEncode(link->acc); char *encode = hashFindVal(thisLink, "needsEncoded"); if (encode != NULL && sameString(encode, "yes")) safef(url, sizeof(url), linktype, encodedAcc); else safef(url, sizeof(url), linktype, link->acc); if (sameString(link->displayVal, "")) printf("<B>%s</B> - <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", label, url, link->acc); else printf("<B>%s</B> - <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", label, url, link->displayVal); } } } sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn2); return attrCnt; } int printGvLink (char *id, int i) { struct gvLink *link = NULL; struct hash *linkInstructions = NULL; struct hash *thisLink = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *linktype, *label; char *doubleEntry = NULL; int attrCnt = 0; hgReadRa(database, organism, rootDir, "links.ra", &linkInstructions); sqlSafef(query, sizeof(query), "select * from hgFixed.gvLink where id = '%s' and attrType = '%s'", id, gvAttrTypeKey[i]); /* attrType == gvAttrTypeKey should be quote safe */ sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct sqlResult *sr2; char **row2; attrCnt++; link = gvLinkLoad(row); /* determine how to do link from .ra file */ thisLink = hashFindVal(linkInstructions, link->raKey); if (thisLink == NULL) continue; /* no link found */ /* type determined by fields: url = external, dataSql = internal, others added later? */ printGvAttrCatType(i); /* only print header if data */ linktype = hashFindVal(thisLink, "dataSql"); label = hashFindVal(thisLink, "label"); if (label == NULL) label = ""; if (linktype != NULL) { sqlSafef(query, sizeof(query), linktype, link->acc); sr2 = sqlGetResult(conn2, query); while ((row2 = sqlNextRow(sr2)) != NULL) { /* should this print more than 1 column, get count from ra? */ if (row2[0] != NULL) { /* print label and result */ printf("<B>%s</B> - %s", label, row2[0]); /* check for link */ doubleEntry = hashFindVal(thisLink, "dataLink"); if (doubleEntry != NULL) { char url[512]; struct hash *newLink; char *accCol = NULL, *format = NULL; int colNum = 1; newLink = hashFindVal(linkInstructions, doubleEntry); accCol = hashFindVal(thisLink, "dataLinkCol"); if (newLink == NULL || accCol == NULL) errAbort("missing required fields in .ra file"); colNum = atoi(accCol); format = hashFindVal(newLink, "url"); safef(url, sizeof(url), format, row2[colNum - 1]); printf(" - <A HREF=\"%s\" TARGET=_blank>%s</A>\n", url, row2[colNum - 1]); } printf("<BR>\n"); } } sqlFreeResult(&sr2); } else { linktype = hashFindVal(thisLink, "url"); if (linktype != NULL) { char url[1024]; char *encodedAcc = cgiEncode(link->acc); char *encode = hashFindVal(thisLink, "needsEncoded"); if (encode != NULL && sameString(encode, "yes")) safef(url, sizeof(url), linktype, encodedAcc); else safef(url, sizeof(url), linktype, link->acc); /* bounce srcLinks through PSU first for disclaimers */ if (sameString(link->attrType, "srcLink")) { char *copy = cgiEncode(url); safef(url, sizeof(url), "http://phencode.bx.psu.edu/cgi-bin/phencode/link-disclaimer?src=%s&link=%s", link->raKey, copy); } if (sameString(link->displayVal, "")) printf("<B>%s</B> - <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", label, url, link->acc); else printf("<B>%s</B> - <A HREF=\"%s\" TARGET=_blank>%s</A><BR>\n", label, url, link->displayVal); } } } sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn2); return attrCnt; } void doOmicia(struct trackDb *tdb, char *itemName) /* this prints the detail page for the Omicia track */ { struct omiciaLink *link = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; /* print generic bed start */ doBed6FloatScore(tdb, itemName); /* print links */ sqlSafef(query, sizeof(query), "select * from omiciaLink where id = '%s'", itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { link = omiciaLinkLoad(row); printLinksRaLink(link->acc, link->raKey, link->displayVal); } sqlFreeResult(&sr); printTrackHtml(tdb); } void doOmiciaOld (struct trackDb *tdb, char *itemName) /* this prints the detail page for the Omicia OMIM track */ { char *table = tdb->table; struct omiciaLink *link = NULL; struct omiciaAttr *attr = NULL; void *omim = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int start = cartInt(cart, "o"); genericHeader(tdb, itemName); printf("<B>Name:</B> %s<BR>\n", itemName); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart = %d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { float score; struct omiciaAuto *om; if (sameString(table, "omiciaAuto")) omim = omiciaAutoLoad(row); else omim = omiciaHandLoad(row); om = (struct omiciaAuto *)omim; printPos(om->chrom, om->chromStart, om->chromEnd, om->strand, TRUE, om->name); /* print score separately, so can divide by 100 to retrieve original */ score = (float)om->score / 100.00; printf("<B>Confidence score:</B> %g<BR>\n", score); } sqlFreeResult(&sr); /* print links */ sqlSafef(query, sizeof(query), "select * from omiciaLink where id = '%s'", itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { link = omiciaLinkLoad(row); printLinksRaLink(link->acc, link->raKey, link->displayVal); } sqlFreeResult(&sr); /* print attributes */ sqlSafef(query, sizeof(query), "select * from omiciaAttr where id = '%s' order by attrType", itemName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { attr = omiciaAttrLoad(row); /* start with simple case print label and value */ printf("<B>%s:</B> %s<BR>\n", attr->attrType, attr->attrVal); } sqlFreeResult(&sr); printTrackHtml(tdb); } void doProtVar (struct trackDb *tdb, char *itemName) /* this prints the detail page for the UniProt variation track */ { char *table = tdb->table; struct protVarPos *mut = NULL; struct protVar *details = NULL; struct protVarAttr attr; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int hasAttr = 0; int i; int start = cartInt(cart, "o"); /* official name, position, band, genomic size */ sqlSafef(query, sizeof(query), "select * from protVar where id = '%s'", itemName); details = protVarLoadByQuery(conn, query); genericHeader(tdb, details->name); /* change label based on species */ if (sameString(organism, "Human")) printf("<B>HGVS name:</B> %s <BR>\n", details->name); else printf("<B>Official name:</B> %s <BR>\n", details->name); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { mut = protVarPosLoad(row); printPos(mut->chrom, mut->chromStart, mut->chromEnd, mut->strand, TRUE, mut->name); } sqlFreeResult(&sr); printf("*Note the DNA retrieved by the above link is the genomic sequence.<br>"); /* print location and mutation type fields */ printf("<B>location:</B> %s<BR>\n", details->location); printf("<B>type:</B> %s<BR>\n", details->baseChangeType); /* add note here about exactness of coordinates */ if (details->coordinateAccuracy == 0) { printf("<B>note:</B> The coordinates for this mutation are only estimated.<BR>\n"); } printf("<DL>"); /* loop through attributes (uses same lists as gv*) */ for(i=0; i<gvAttrSize; i++) { /* check 2 attribute tables for each type */ sqlSafef(query, sizeof(query), "select * from protVarAttr where id = '%s' and attrType = '%s'", itemName, gvAttrTypeKey[i]); /* attrType == gvAttrTypeKey should be quote safe */ sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hasAttr++; protVarAttrStaticLoad(row, &attr); printGvAttrCatType(i); /* only print header, if data */ /* print value */ printf("%s<BR>", attr.attrVal); } sqlFreeResult(&sr); hasAttr += printProtVarLink(itemName, i); } if (hasAttr > 0) printf("</DD>"); printf("</DL>\n"); protVarPosFree(&mut); freeMem(gvPrevCat); freeMem(gvPrevType); printTrackHtml(tdb); hFreeConn(&conn); } void doGv(struct trackDb *tdb, char *itemName) /* this prints the detail page for the Genome variation track */ { char *table = tdb->table; struct gvPos *mut = NULL; struct gv *details = NULL; struct gvAttr attr; struct gvAttrLong attrLong; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; int hasAttr = 0; int i; int start = cartInt(cart, "o"); /* official name, position, band, genomic size */ sqlSafef(query, sizeof(query), "select * from hgFixed.gv where id = '%s'", itemName); details = gvLoadByQuery(conn, query); genericHeader(tdb, details->name); /* change label based on species */ if (sameString(organism, "Human")) printf("<B>HGVS name:</B> %s <BR>\n", details->name); else printf("<B>Official name:</B> %s <BR>\n", details->name); sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and " "chromStart=%d and name = '%s'", table, seqName, start, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { char *strand = NULL; mut = gvPosLoad(row); strand = mut->strand; printPos(mut->chrom, mut->chromStart, mut->chromEnd, strand, TRUE, mut->name); } sqlFreeResult(&sr); if (mut == NULL) errAbort("Couldn't find variant %s at %s %d", itemName, seqName, start); printf("*Note the DNA retrieved by the above link is the genomic sequence.<br>"); /* fetch and print the source */ sqlSafef(query, sizeof(query), "select * from hgFixed.gvSrc where srcId = '%s'", details->srcId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct gvSrc *src = gvSrcLoad(row); printf("<B>source:</B> %s", src->lsdb); printf("<BR>\n"); } sqlFreeResult(&sr); /* print location and mutation type fields */ printf("<B>location:</B> %s<BR>\n", details->location); printf("<B>type:</B> %s<BR>\n", details->baseChangeType); /* add note here about exactness of coordinates */ if (details->coordinateAccuracy == 0) { printf("<B>note:</B> The coordinates for this mutation are only estimated.<BR>\n"); } printf("<DL>"); /* loop through attributes */ for(i=0; i<gvAttrSize; i++) { /* check all 3 attribute tables for each type */ sqlSafef(query, sizeof(query), "select * from hgFixed.gvAttrLong where id = '%s' and attrType = '%s'", itemName, gvAttrTypeKey[i]); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hasAttr++; gvAttrLongStaticLoad(row, &attrLong); printGvAttrCatType(i); /* only print header, if data */ /* print value */ printf("%s<BR>", attrLong.attrVal); } sqlFreeResult(&sr); sqlSafef(query, sizeof(query), "select * from hgFixed.gvAttr where id = '%s' and attrType = '%s'", itemName, gvAttrTypeKey[i]); /* attrType == gvAttrTypeKey should be quote safe */ sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hasAttr++; gvAttrStaticLoad(row, &attr); printGvAttrCatType(i); /* only print header, if data */ /* print value */ printf("%s<BR>", attr.attrVal); } sqlFreeResult(&sr); hasAttr += printGvLink(itemName, i); } if (hasAttr > 0) printf("</DD>"); printf("</DL>\n"); /* split code from printTrackHtml */ printTBSchemaLink(tdb); printOrigAssembly(tdb); printDataVersion(database, tdb); printUpdateTime(database, tdb, NULL); if (tdb->html != NULL && tdb->html[0] != 0) { htmlHorizontalLine(); puts(tdb->html); } hPrintf("<BR>\n"); gvPosFree(&mut); freeMem(gvPrevCat); freeMem(gvPrevType); //printTrackHtml(tdb); hFreeConn(&conn); } void doPgSnp(struct trackDb *tdb, char *itemName, struct customTrack *ct) /* print detail page for personal genome track (pgSnp) */ { char *table; struct sqlConnection *conn; struct sqlResult *sr; char **row; char query[256]; if (ct == NULL) { table = tdb->table; conn = hAllocConn(database); } else { table = ct->dbTableName; conn = hAllocConn(CUSTOM_TRASH); //ct->tdb } genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, itemName, seqName, cartInt(cart, "o")); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct pgSnp *el = pgSnpLoad(row); char *all[8]; char *freq[8]; char *score[8]; char *name = cloneString(el->name); char *fr = NULL; char *sc = NULL; char *siftTab = trackDbSetting(tdb, "pgSiftPredTab"); char *polyTab = trackDbSetting(tdb, "pgPolyphenPredTab"); int i = 0; printPos(el->chrom, el->chromStart, el->chromEnd, "+", TRUE, el->name); printf("Alleles are relative to forward strand of reference genome:<br>\n"); printf("<table class=\"descTbl\">" "<tr><th>Allele</th><th>Frequency</th><th>Quality Score</th></tr>\n"); chopByChar(name, '/', all, el->alleleCount); if (differentString(el->alleleFreq, "")) { fr = cloneString(el->alleleFreq); chopByChar(fr, ',', freq, el->alleleCount); } if (el->alleleScores != NULL) { sc = cloneString(el->alleleScores); chopByChar(sc, ',', score, el->alleleCount); } for (i=0; i < el->alleleCount; i++) { if (sameString(el->alleleFreq, "") || sameString(freq[i], "0")) freq[i] = "not available"; if (sc == NULL || sameString(sc, "")) score[i] = "not available"; printf("<tr><td>%s</td><td>%s</td><td>%s</td></tr>", all[i], freq[i], score[i]); } printf("</table>"); if (!trackHubDatabase(database)) printPgDbLink(database, tdb, el); if (siftTab != NULL) printPgSiftPred(database, siftTab, el); if (polyTab != NULL) printPgPolyphenPred(database, polyTab, el); char *genePredTable = "knownGene"; if (!trackHubDatabase(database)) printSeqCodDisplay(database, el, genePredTable); } sqlFreeResult(&sr); printTrackHtml(tdb); hFreeConn(&conn); } void doPgPhenoAssoc(struct trackDb *tdb, char *itemName) { char *table = tdb->table; struct pgPhenoAssoc *pheno = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct dyString *query = dyStringNew(512); int start = cartInt(cart, "o"); genericHeader(tdb, itemName); sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); sqlDyStringPrintf(query, "name = '%s' and chromStart = %d", itemName, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { pheno = pgPhenoAssocLoad(row); bedPrintPos((struct bed *)pheno, 4, tdb); printf("Personal Genome phenotype: <a href=\"%s\">link to phenotype source</a><BR>\n", pheno->srcUrl); } printTrackHtml(tdb); } void doAllenBrain(struct trackDb *tdb, char *itemName) /* Put up page for Allen Brain Atlas. */ { char *table = tdb->table; struct psl *pslList; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char *url, query[512]; genericHeader(tdb, itemName); sqlSafef(query, sizeof(query), "select url from allenBrainUrl where name = '%s'", itemName); url = sqlQuickString(conn, query); printf("<H3><A HREF=\"%s\" target=_blank>", url); printf("Click here to open Allen Brain Atlas on this probe.</A></H3><BR>"); pslList = getAlignments(conn, table, itemName); puts("<H3>Probe/Genome Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", table, itemName); printTrackHtml(tdb); hFreeConn(&conn); } void doExaptedRepeats(struct trackDb *tdb, char *itemName) /* Respond to click on the exaptedRepeats track. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *chr, *name; unsigned int chromStart, chromEnd; boolean blastzAln; cartWebStart(cart, database, "%s", itemName); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, itemName); selectOneRow(conn, tdb->table, query, &sr, &row); chr = cloneString(row[0]); chromStart = sqlUnsigned(row[1]); chromEnd = sqlUnsigned(row[2]); name = cloneString(row[3]); blastzAln = (sqlUnsigned(row[4])==1); printPos(chr, chromStart, chromEnd, NULL, TRUE, name); printf("<B>Item:</B> %s<BR>\n", name); if(blastzAln){printf("<B>Alignment to the repeat consensus verified with blastz:</B> yes<BR>\n");} else{printf("<B>Alignment to repeat consensus verified with blastz:</B> no<BR>\n");} sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doIgtc(struct trackDb *tdb, char *itemName) /* Details for International Gene Trap Consortium. */ { char *name = cloneString(itemName); char *source = NULL; char *encodedName = cgiEncode(itemName); cgiDecode(name, name, strlen(name)); source = strrchr(name, '_'); if (source == NULL) source = "Unknown"; else source++; genericHeader(tdb, name); printf("<B>Source:</B> %s<BR>\n", source); printCustomUrl(tdb, name, TRUE); if (startsWith("psl", tdb->type)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; struct dyString *query = dyStringNew(512); char **row = NULL; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); sqlDyStringPrintf(query, "select * from %s where tName = '%s' and ", tdb->table, seqName); if (rowOffset) hAddBinToQuery(start, end, query); sqlDyStringPrintf(query, "tStart = %d and qName = '%s'", start, itemName); sr = sqlGetResult(conn, query->string); if ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row+rowOffset); printPos(psl->tName, psl->tStart, psl->tEnd, psl->strand, TRUE, psl->qName); if (hGenBankHaveSeq(database, itemName, NULL)) { printf("<H3>%s/Genomic Alignments</H3>", name); printAlignments(psl, start, "htcCdnaAli", tdb->table, encodedName); } else { printf("<B>Alignment details:</B>\n"); pslDumpHtml(psl); } pslFree(&psl); } sqlFreeResult(&sr); hFreeConn(&conn); } else warn("Unsupported type \"%s\" for IGTC (expecting psl).", tdb->type); printTrackHtml(tdb); } void doRdmr(struct trackDb *tdb, char *item) /* details page for rdmr track */ { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; int ii; char *chrom,*chromStart,*chromEnd,*fibroblast,*iPS,*absArea,*gene,*dist2gene,*relation2gene,*dist2island,*relation2island,*fdr; genericHeader(tdb, item); sqlSafef(query, sizeof(query), "select chrom,chromStart,chromEnd,fibroblast,iPS,absArea,gene,dist2gene,relation2gene,dist2island,relation2island,fdr from rdmrRaw where gene = '%s'", item); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); ii = 0; chrom = row[ii];ii++; chromStart = row[ii];ii++; chromEnd = row[ii];ii++; fibroblast = row[ii];ii++; iPS = row[ii];ii++; absArea = row[ii];ii++; gene = row[ii];ii++; dist2gene = row[ii];ii++; relation2gene = row[ii];ii++; dist2island = row[ii];ii++; relation2island = row[ii];ii++; fdr = row[ii]; printf("<B>Closest Gene:</B> %s\n", gene);fflush(stdout); printf("<BR><B>Genomic Position:</B> %s:%s-%s", chrom, chromStart, chromEnd); printf("<BR><B>Fibroblast M value:</B> %s\n", fibroblast); printf("<BR><B>iPS M value:</B> %s\n", iPS); printf("<BR><B>Absolute area:</B> %s", absArea); printf("<BR><B>Distance to gene:</B> %s\n", dist2gene); printf("<BR><B>Relation to gene:</B> %s\n", relation2gene); printf("<BR><B>Distance to CGI:</B> %s\n", dist2island); printf("<BR><B>Relation to CGI:</B> %s\n", relation2island); printf("<BR><B>False discovery rate:</B> %s\n", fdr); sqlFreeResult(&sr); printTrackHtml(tdb); hFreeConn(&conn); } void doKomp(struct trackDb *tdb, char *item) /* KnockOut Mouse Project */ { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; genericHeader(tdb, item); char defaultExtra[HDB_MAX_TABLE_STRING]; safef(defaultExtra, sizeof(defaultExtra), "%sExtra", tdb->table); char *extraTable = trackDbSettingOrDefault(tdb, "xrefTable", defaultExtra); boolean gotExtra = sqlTableExists(conn, extraTable); if (gotExtra) { char mgiId[256]; sqlSafef(query, sizeof(query), "select alias from %s where name = '%s'", extraTable, item); sqlQuickQuery(conn, query, mgiId, sizeof(mgiId)); char *ptr = strchr(mgiId, ','); if (!startsWith("MGI:", mgiId) || ptr == NULL) errAbort("Where is the MGI ID?: '%s'", mgiId); else *ptr = '\0'; // Use the MGI ID to show all centers that are working on this gene: sqlSafef(query, sizeof(query), "select name,alias from %s where alias like '%s,%%'", extraTable, mgiId); sr = sqlGetResult(conn, query); char lastMgiId[16]; lastMgiId[0] = '\0'; puts("<TABLE BORDERWIDTH=0 CELLPADDING=0>"); while ((row = sqlNextRow(sr)) != NULL) { char *words[3]; int wordCount = chopCommas(row[1], words); if (wordCount >= 3) { char *mgiId = words[0], *center = words[1], *status = words[2]; if (!sameString(mgiId, lastMgiId)) { printf("<TR><TD colspan=2>"); printCustomUrl(tdb, mgiId, FALSE); printf("</TD></TR>\n<TR><TD colspan=2>"); printOtherCustomUrl(tdb, mgiId, "mgiUrl", FALSE); printf("</TD></TR>\n"); safecpy(lastMgiId, sizeof(lastMgiId), mgiId); } printf("<TR><TD><B>Center: </B>%s</TD>\n", center); ptr = strrchr(row[0], '_'); if (ptr != NULL) printf("<TD><B>Design ID: </B>%s</TD>\n", ptr+1); printf("<TD><B>Status: </B>%s", status); if ((ptr != NULL) && (strstr(status, "vailable") != NULL)) { char *productStr; char *chp; productStr = strdup(status); chp = strstr(productStr, "vailable"); chp--; chp--; *chp = '\0'; printf(" (<A HREF=\"http://www.knockoutmouse.org/search_results?criteria=%s\" target=_blank>", ++ptr); printf("order %s)", productStr);fflush(stdout); } printf("</TD></TR>\n"); } } puts("<TR><TD colspan=2>"); sqlFreeResult(&sr); } sqlSafef(query, sizeof(query), "select chrom,chromStart,chromEnd from %s " "where name = '%s'", tdb->table, item); sr = sqlGetResult(conn, query); char lastChr[32]; int lastStart = -1; int lastEnd = -1; lastChr[0] = '\0'; while ((row = sqlNextRow(sr)) != NULL) { char *chr = row[0]; int start = atoi(row[1]), end = atoi(row[2]); if (!sameString(chr, lastChr) || start != lastStart || end != lastEnd) printPos(chr, start, end, NULL, TRUE, item); safecpy(lastChr, sizeof(lastChr), chr); lastStart = start; lastEnd = end; } sqlFreeResult(&sr); if (gotExtra) puts("</TD></TR></TABLE>"); printTrackHtml(tdb); hFreeConn(&conn); } void doHgIkmc(struct trackDb *tdb, char *item) /* Human Genome Map of KnockOut Mouse Project */ { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; genericHeader(tdb, item); char defaultExtra[HDB_MAX_TABLE_STRING]; safef(defaultExtra, sizeof(defaultExtra), "%sExtra", tdb->table); char *extraTable = trackDbSettingOrDefault(tdb, "xrefTable", defaultExtra); boolean gotExtra = sqlTableExists(conn, extraTable); if (gotExtra) { char mgiId[256]; char *designId; sqlSafef(query, sizeof(query), "select alias from %s where name = '%s'", extraTable, item); sqlQuickQuery(conn, query, mgiId, sizeof(mgiId)); char *ptr = strchr(mgiId, ','); if (!startsWith("MGI:", mgiId) || ptr == NULL) errAbort("Where is the MGI ID?: '%s'", mgiId); else *ptr = '\0'; ptr++; designId = ptr; ptr = strchr(ptr, ','); *ptr = '\0'; // Show entries with the MGI ID and design ID sqlSafef(query, sizeof(query), "select name,alias from %s where alias like '%s,%s%%'", extraTable, mgiId, designId); sr = sqlGetResult(conn, query); char lastMgiId[16]; lastMgiId[0] = '\0'; puts("<TABLE BORDERWIDTH=0 CELLPADDING=0>"); while ((row = sqlNextRow(sr)) != NULL) { char *words[4]; int wordCount = chopCommas(row[1], words); if (wordCount >= 3) { char *mgiId = words[0], *center = words[2], *status = words[3]; if (!sameString(mgiId, lastMgiId)) { printf("<TR><TD colspan=2>"); printCustomUrl(tdb, mgiId, FALSE); printf("</TD></TR>\n<TR><TD colspan=2>"); printOtherCustomUrl(tdb, mgiId, "mgiUrl", FALSE); printf("</TD></TR>\n"); safecpy(lastMgiId, sizeof(lastMgiId), mgiId); } printf("<TR><TD><B>Center: </B>%s</TD>\n", center); ptr = strrchr(row[0], '_'); if (ptr != NULL) printf("<TD><B>Design ID: </B>%s</TD>\n", ptr+1); printf("<TD><B>Status: </B>%s", status); if ((ptr != NULL) && (strstr(status, "vailable") != NULL)) { char *productStr; char *chp; productStr = strdup(status); chp = strstr(productStr, "vailable"); chp--; chp--; *chp = '\0'; printf(" (<A HREF=\"http://www.komp.org/geneinfo.php?project=%s\" target=_blank>", ++ptr); printf("order %s)", productStr);fflush(stdout); } printf("</TD></TR>\n"); } } puts("<TR><TD colspan=2>"); sqlFreeResult(&sr); } sqlSafef(query, sizeof(query), "select chrom,chromStart,chromEnd from %s " "where name = '%s'", tdb->table, item); sr = sqlGetResult(conn, query); char lastChr[32]; int lastStart = -1; int lastEnd = -1; lastChr[0] = '\0'; while ((row = sqlNextRow(sr)) != NULL) { char *chr = row[0]; int start = atoi(row[1]), end = atoi(row[2]); if (!sameString(chr, lastChr) || start != lastStart || end != lastEnd) printPos(chr, start, end, NULL, TRUE, item); safecpy(lastChr, sizeof(lastChr), chr); lastStart = start; lastEnd = end; } sqlFreeResult(&sr); if (gotExtra) puts("</TD></TR></TABLE>"); printTrackHtml(tdb); hFreeConn(&conn); } void doUCSFDemo(struct trackDb *tdb, char *item) { genericHeader(tdb, item); printf("<B>Name:</B> %s<BR>\n", item); /* this prints the detail page for the clinical information for Cancer Demo datasets */ char *table = tdb->table; char *cliniTable=NULL, *key=NULL; char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; if (sameString(table, "CGHBreastCancerUCSF") || sameString(table, "expBreastCancerUCSF")) { cliniTable = "phenBreastTumors"; key = "id"; /* er, pr */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>ER</TH> <TH>PR</TH></TR>\n"); sqlSafef(query, sizeof(query), "select er, pr from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* subEuc, subCor */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>subEuc</TH> <TH>subCor</TH></TR>\n"); sqlSafef(query, sizeof(query), "select subEuc, subCor from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* subtypes */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>subtype2</TH> <TH>subtype3</TH> <TH>subtype4</TH> <TH>subtype5</TH></TR>\n"); sqlSafef(query, sizeof(query), "select subtype2, subtype3, subtype4, subtype5 from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("<TD>%s</TD>", row[2]); printf("<TD>%s</TD>", row[3]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* stage, size, nodalStatus, SBRGrade */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>Stage</TH> <TH>Size</TH> <TH>Nodal status</TH> <TH>SBR Grade</TH></TR>\n"); sqlSafef(query, sizeof(query), "select stage, size, nodalStatus, SBRGrade from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("<TD>%s</TD>", row[2]); printf("<TD>%s</TD>", row[3]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* race, familyHistory, ageDx */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>Race</TH> <TH>Family history</TH> <TH>Age of Diagnosis</TH> </TR>\n"); sqlSafef(query, sizeof(query), "select race, familyHistory, ageDx from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("<TD>%s</TD>", row[2]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* rad, chemo, horm, erb, p53, ki67 */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>Rad</TH> <TH>Chemo</TH> <TH>Horm</TH> <TH>ERB</TH> <TH>p53</TH>"); printf("<TH>ki67</TH></TR>\n"); sqlSafef(query, sizeof(query), "select rad, chemo, horm, erb, p53, ki67 from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("<TD>%s</TD>", row[2]); printf("<TD>%s</TD>", row[3]); printf("<TD>%s</TD>", row[4]); printf("<TD>%s</TD>", row[5]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* T/N/M */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>T</TH> <TH>N</TH> <TH>M</TH></TR>\n"); sqlSafef(query, sizeof(query), "select T, N, M from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR>"); printf("<TD>%s</TD>", row[0]); printf("<TD>%s</TD>", row[1]); printf("<TD>%s</TD>", row[2]); printf("</TR>"); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* times */ printf("<BR><B>Times:</B><BR>\n"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>Type</TH> <TH>Binary</TH> <TH>Value</TH></TR>\n"); sqlSafef(query, sizeof(query), "select overallBinary, overallTime, diseaseBinary, diseaseTime, " "allrecBinary, allrecTime, distrecBinary, distrecTime from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<TR><TD>Overall</TD> <TD>%s</TD> <TD>%s</TD></TR>", row[0], row[1]); printf("<TR><TD>Disease</TD> <TD>%s</TD> <TD>%s</TD></TR>", row[2], row[3]); printf("<TR><TD>Allrec</TD> <TD>%s</TD> <TD>%s</TD></TR>", row[4], row[5]); printf("<TR><TD>Distrec</TD> <TD>%s</TD> <TD>%s</TD></TR>", row[6], row[7]); } printf("</TABLE>\n"); sqlFreeResult(&sr); /* affyChipId */ printf("<BR>"); sqlSafef(query, sizeof(query), "select affyChipId from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Affy Chip ID:</B> %s\n", row[0]); } printf("</TABLE>\n"); sqlFreeResult(&sr); return; } else if ( sameString(table, "cnvLungBroadv2")) { cliniTable = "tspLungClinical"; key = "tumorID"; } else return; htmlHorizontalLine(); sqlSafef(query, sizeof(query), "select * from %s where %s = '%s' ", cliniTable, key,item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { int numFields = sqlCountColumns(sr); int i; char *fieldName=NULL, *value=NULL; for (i=0; i< numFields; i++) { fieldName = sqlFieldName(sr); value = row[i]; printf("%s: <B>%s</B><BR>\n", fieldName, value); } } sqlFreeResult(&sr); //printTrackHtml(tdb); //hFreeConn } void doConsIndels(struct trackDb *tdb, char *item) /* Display details about items in the Indel-based Conservation track. */ { struct dyString *dy = dyStringNew(1024); struct sqlConnection *conn = hAllocConn(database); struct itemConf *cf; char confTable[128]; /* create name for confidence table containing posterior probability and false discovery rate (FDR). */ safef(confTable, sizeof(confTable), "%sConf", tdb->table); if (sqlTableExists(conn, confTable)) { /* print the posterior probability and FDR if available */ struct sqlResult *sr; char query[256], **row; sqlSafef(query, sizeof(query), "select * from %s where id = '%s'", confTable, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cf = itemConfLoad(row); dyStringPrintf(dy, "<B>Posterior Probability:</B> %.4g<BR>\n", cf->probability); dyStringPrintf(dy, "<B>False Discovery Rate (FDR):</B> %.2f<BR>\n", cf->fdr); itemConfFree(&cf); } sqlFreeResult(&sr); } hFreeConn(&conn); genericClickHandlerPlus(tdb, item, NULL, dy->string); dyStringFree(&dy); } #define KIDD_EICHLER_DISC_PREFIX "kiddEichlerDisc" void printKiddEichlerNcbiLinks(struct trackDb *tdb, char *item) /* If we have a table that maps kiddEichler IDs to NCBI IDs, print links. */ { char *ncbiAccXref = trackDbSetting(tdb, "ncbiAccXref"); if (isNotEmpty(ncbiAccXref) && hTableExists(database, ncbiAccXref)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char *cloneName = cloneString(item); char *postUnderscore = strchr(cloneName, '_'); char query[512]; /* In kiddEichlerDiscG248, all clone names have a WIBR2-\w+_ prefix * before the G248\w+ clone name given in the files used to make this * table, e.g. WIBR2-1962P18_G248P85919H9,transchrm_chr4 -- skip that * prefix. Then strip all kiddEichlerDisc* names' ,.* suffixes. */ if (startsWith("WIBR2-", cloneName) && postUnderscore != NULL) cloneName = postUnderscore+1; chopPrefixAt(cloneName, ','); sqlSafef(query, sizeof(query), "select cloneAcc, endF, endR from %s where name = '%s'", ncbiAccXref, cloneName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if (isNotEmpty(row[0])) printf("<B>Clone Report and Sequence (NCBI Nucleotide): </B>" "<A HREF=\"%s\" TARGET=_BLANK>%s</A><BR>\n", getEntrezNucleotideUrl(row[0]), row[0]); char *endUrlFormat = trackDbSetting(tdb, "pairedEndUrlFormat"); /* Truncate cloneName to get library name: ABC* are followed by _, * G248 are not. */ char *libId = cloneName; if (startsWith("G248", libId)) libId[strlen("G248")] = '\0'; else if (startsWith("ABC", libId)) chopPrefixAt(libId, '_'); if (endUrlFormat && differentStringNullOk(row[1], "0")) { printf("<B>Forward End Read (NCBI Trace Archive): </B>" "<A HREF=\""); printf(endUrlFormat, libId, row[1]); printf("\" TARGET=_BLANK>%s</A><BR>\n", row[1]); } if (endUrlFormat && differentStringNullOk(row[2], "0")) { printf("<B>Reverse End Read (NCBI Trace Archive): </B>" "<A HREF=\""); printf(endUrlFormat, libId, row[2]); printf("\" TARGET=_BLANK>%s</A><BR>\n", row[2]); } } sqlFreeResult(&sr); hFreeConn(&conn); } } void doKiddEichlerDisc(struct trackDb *tdb, char *item) /* Discordant clone end mappings from Kidd..Eichler 2008. */ { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; boolean hasBin; struct bed *bed; boolean firstTime = TRUE; int start = cartInt(cart, "o"); genericHeader(tdb, item); if (! startsWith(KIDD_EICHLER_DISC_PREFIX, tdb->table)) errAbort("track tableName must begin with "KIDD_EICHLER_DISC_PREFIX " but instead it is %s", tdb->table); hasBin = hOffsetPastBin(database, seqName, tdb->table); /* We don't need to add bin to this because name is indexed: */ sqlSafef(query, sizeof(query), "select * from %s where name = '%s' " "and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); int lastBlk = bed->blockCount - 1; int endForUrl = (bed->chromStart + bed->chromStarts[lastBlk] + bed->blockSizes[lastBlk]); char *endFudge = trackDbSetting(tdb, "endFudge"); if (endFudge && !strstr(bed->name, "OEA")) endForUrl += atoi(endFudge); char sampleName[16]; safecpy(sampleName, sizeof(sampleName), tdb->table + strlen(KIDD_EICHLER_DISC_PREFIX)); touppers(sampleName); char itemPlus[2048]; safef(itemPlus, sizeof(itemPlus), "%s&o=%d&t=%d&g=%s_discordant&%s_discordant=full", cgiEncode(item), start, endForUrl, sampleName, sampleName); printCustomUrlWithLabel(tdb, itemPlus, item, "url", FALSE, NULL); printKiddEichlerNcbiLinks(tdb, bed->name); printf("<B>Score:</B> %d<BR>\n", bed->score); printPosOnChrom(bed->chrom, bed->chromStart, bed->chromEnd, bed->strand, TRUE, bed->name); } sqlFreeResult(&sr); printTrackHtml(tdb); } void doBedDetail(struct trackDb *tdb, struct customTrack *ct, char *itemName) /* generate the detail page for a custom track of bedDetail type */ { char *table; struct bedDetail *r = NULL; struct sqlConnection *conn; struct sqlResult *sr; char **row; char query[256]; char *chrom = cartString(cart,"c"); /* don't assume name is unique */ int start = cgiInt("o"); int end = cgiInt("t"); int bedPart = 4; if (ct == NULL) { char *words[3]; int cnt = chopLine(cloneString(tdb->type), words); if (cnt > 1) bedPart = atoi(words[1]) - 2; table = tdb->table; conn = hAllocConn(database); genericHeader(tdb, itemName); } else { table = ct->dbTableName; conn = hAllocConn(CUSTOM_TRASH); bedPart = ct->fieldCount - 2; /* header handled by custom track handler */ } /* postion, band, genomic size */ sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and chromEnd = %d and name = '%s'", table, chrom, start, end, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { r = bedDetailLoadWithGaps(row, bedPart+2); if (isNotEmpty(r->id)) { printCustomUrl(tdb, r->id, TRUE); printf("<br>\n"); } bedPrintPos((struct bed*)r, bedPart, tdb); printf("<br>"); if (isNotEmpty(r->id) && !sameString("qPcrPrimers", table)) printf("<B>ID:</B> %s <BR>\n", r->id); if (isNotEmpty(r->description)) printf("%s <BR>\n", r->description); } sqlFreeResult(&sr); /* do not print this for custom tracks, they do this later */ if (ct == NULL) printTrackHtml(tdb); bedDetailFree(&r); hFreeConn(&conn); } struct trackDb *tdbForTableArg() /* get trackDb for track passed in table arg */ { char *table = cartString(cart, "table"); struct trackDb *tdb = hashFindVal(trackHash, table); if (tdb == NULL) errAbort("no trackDb entry for %s", table); return tdb; } void doQPCRPrimers(struct trackDb *tdb, char *itemName) /* Put up page for QPCRPrimers. */ { genericHeader(tdb, itemName); doBedDetail(tdb, NULL, itemName); } /* end of doQPCRPrimers */ void doSnakeClick(struct trackDb *tdb, char *itemName) /* Put up page for snakes. */ { struct trackDb *parentTdb = trackDbTopLevelSelfOrParent(tdb); char *otherSpecies = trackDbSetting(tdb, "otherSpecies"); if (otherSpecies == NULL) otherSpecies = trackHubSkipHubName(tdb->table) + strlen("snake"); char *hubName = cloneString(database); char otherDb[4096]; char *qName = cartOptionalString(cart, "qName"); int qs = atoi(cartOptionalString(cart, "qs")); int qe = atoi(cartOptionalString(cart, "qe")); int qWidth = atoi(cartOptionalString(cart, "qWidth")); char *qTrack = cartString(cart, "g"); if(isHubTrack(qTrack) && ! trackHubDatabase(database)) hubName = cloneString(qTrack); /* current mouse strain hal file has incorrect chrom names */ char *aliasQName = qName; // aliasQName = "chr1"; // temporarily make this work for the mouse hal if(trackHubDatabase(database) || isHubTrack(qTrack)) { char *ptr = strchr(hubName + 4, '_'); *ptr = 0; safef(otherDb, sizeof otherDb, "%s_%s", hubName, otherSpecies); } else { safef(otherDb, sizeof otherDb, "%s", otherSpecies); } char headerText[256]; safef(headerText, sizeof headerText, "reference: %s, query: %s\n", trackHubSkipHubName(database), trackHubSkipHubName(otherDb) ); genericHeader(parentTdb, headerText); printf("<A HREF=\"hgTracks?db=%s&position=%s:%d-%d&%s_snake%s=full\" TARGET=_BLANK>%s:%d-%d</A> link to block in query assembly: <B>%s</B></A><BR>\n", otherDb, aliasQName, qs, qe, hubName, trackHubSkipHubName(database), aliasQName, qs, qe, trackHubSkipHubName(otherDb)); int qCenter = (qs + qe) / 2; int newQs = qCenter - qWidth/2; int newQe = qCenter + qWidth/2; printf("<A HREF=\"hgTracks?db=%s&position=%s:%d-%d&%s_snake%s=full\" TARGET=\"_blank\">%s:%d-%d</A> link to same window size in query assembly: <B>%s</B></A><BR>\n", otherDb, aliasQName, newQs, newQe,hubName, trackHubSkipHubName(database), aliasQName, newQs, newQe, trackHubSkipHubName(otherDb) ); printTrackHtml(tdb); } bool vsameWords(char *a, va_list args) /* returns true if a is sameWord as any arg, all args must be char* */ { bool found = FALSE; char *b; while ((b = va_arg(args, char *)) != NULL) { if (sameWord(a, b)) { found = TRUE; break; } } return found; } bool sameAltWords(char *a, char *b, ...) /* returns true if a is sameWord as any of the variables or b is sameWord as any of them */ { va_list args; va_start(args, b); bool res = vsameWords(a, args); va_end(args); if (!res && (b != NULL)) { va_start(args, b); res = vsameWords(b, args); va_end(args); } return res; } bool sameWords(char *a, ...) /* returns true if a is equal to any b */ { va_list args; va_start(args, a); bool res = vsameWords(a, args); va_end(args); return res; } void printAddWbr(char *text, int distance) /* a crazy hack for firefox/mozilla that is unable to break long words in tables * We need to add a <wbr> tag every x characters in the text to make text breakable. */ { int i; i = 0; char *c; c = text; bool doNotBreak = FALSE; while (*c != 0) { if ((*c=='&') || (*c=='<')) doNotBreak = TRUE; if (*c==';' || (*c =='>')) doNotBreak = FALSE; printf("%c", *c); if (i % distance == 0 && ! doNotBreak) printf("<wbr>"); c++; i++; } } static char *replaceSuffix(char *input, char *newSuffix) /* Given a filename with a suffix, replace existing suffix with a new suffix. */ { char buffer[4096]; safecpy(buffer, sizeof buffer, input); char *dot = strrchr(buffer, '.'); safecpy(dot+1, sizeof buffer - 1 - (dot - buffer), newSuffix); return cloneString(buffer); } static void makeBigPsl(char *pslName, char *faName, char *db, char *outputBigBed) /* Make a bigPsl with the blat results. */ { char *bigPslFile = replaceSuffix(outputBigBed, "bigPsl"); char cmdBuffer[4096]; safef(cmdBuffer, sizeof(cmdBuffer), "loader/pslToBigPsl %s -fa=%s stdout | sort -k1,1 -k2,2n > %s", pslName, faName, bigPslFile); system(cmdBuffer); char buf[4096]; char *twoBitDir; if (trackHubDatabase(db)) { struct trackHubGenome *genome = trackHubGetGenome(db); twoBitDir = genome->twoBitPath; } else { safef(buf, sizeof(buf), "/gbdb/%s", db); twoBitDir = hReplaceGbdbSeqDir(buf, db); safef(buf, sizeof(buf), "%s%s.2bit", twoBitDir, db); twoBitDir = buf; } safef(cmdBuffer, sizeof(cmdBuffer), "loader/bedToBigBed -verbose=0 -udcDir=%s -extraIndex=name -sizesIs2Bit -tab -as=loader/bigPsl.as -type=bed9+16 %s %s %s", udcDefaultDir(), bigPslFile, twoBitDir, outputBigBed); system(cmdBuffer); unlink(bigPslFile); } static void buildBigPsl(char *fileNames) /* Build a custom track with a bigPsl file out of blat results. * Bring up the bigPsl detail page with all the alignments. */ { char *trackName = cartString(cart, "trackName"); char *trackDescription = cartString(cart, "trackDescription"); char *pslName, *faName, *qName; parseSs(fileNames, &pslName, &faName, &qName); struct tempName bigBedTn; trashDirDateFile(&bigBedTn, "hgBlat", "bp", ".bb"); char *bigBedFile = bigBedTn.forCgi; makeBigPsl(pslName, faName, database, bigBedFile); char* host = getenv("HTTP_HOST"); boolean isProt = cgiOptionalString("isProt") != NULL; char *customTextTemplate = "track type=bigPsl indelDoubleInsert=on indelQueryInsert=on pslFile=%s visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=%s name=\"%s\" description=\"%s\"\n"; char *extraForMismatch = "indelPolyA=on showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases"; if (isProt) extraForMismatch = ""; char buffer[4096]; safef(buffer, sizeof buffer, customTextTemplate, bigBedTn.forCgi, host, extraForMismatch, bigBedTn.forCgi, trackName, trackDescription); struct customTrack *ctList = getCtList(); struct customTrack *newCts = customFactoryParse(database, buffer, FALSE, NULL); theCtList = customTrackAddToList(ctList, newCts, NULL, FALSE); customTracksSaveCart(database, cart, theCtList); cartSetString(cart, "i", "PrintAllSequences"); hgCustom(newCts->tdb->track, NULL); } void doMiddle() /* Generate body of HTML. */ { char *track = cartString(cart, "g"); char *item = cloneString(cartOptionalString(cart, "i")); char *parentWigMaf = cartOptionalString(cart, "parentWigMaf"); struct trackDb *tdb = NULL; hgBotDelayFrac(0.5); /* database and organism are global variables used in many places */ getDbAndGenome(cart, &database, &genome, NULL); organism = hOrganism(database); scientificName = hScientificName(database); initGenbankTableNames(database); dbIsFound = trackHubDatabase(database) || sqlDatabaseExists(database); // Try to deal with virt chrom position used by hgTracks. // Hack the cart vars to set to a non virtual chrom mode position if (sameString("virt", cartString(cart, "c")) || sameString("getDna", cartUsualString(cart, "g", "")) ) { char *nvPos = cartUsualString(cart, "nonVirtPosition", NULL); if (nvPos) { // parse non-virtual position char *pos = cloneString(nvPos); char *colon = strchr(pos, ':'); if (!colon) errAbort("position has no colon"); char *dash = strchr(pos, '-'); if (!dash) errAbort("position has no dash"); *colon = 0; *dash = 0; char *chromName = cloneString(pos); int winStart = atol(colon+1) - 1; int winEnd = atol(dash+1); cartSetString(cart, "position", nvPos); cartSetString(cart, "c", chromName); cartSetInt(cart, "l", winStart); cartSetInt(cart, "r", winEnd); } } if (dbIsFound) seqName = hgOfficialChromName(database, cartString(cart, "c")); else seqName = cartString(cart, "c"); winStart = cartUsualInt(cart, "l", 0); winEnd = cartUsualInt(cart, "r", 0); /* Allow faked-out c=0 l=0 r=0 (e.g. for unaligned mRNAs) but not just any * old bogus position: */ if (seqName == NULL) { if (winStart != 0 || winEnd != 0) webAbortNoHttpHeader("CGI variable error", "hgc: bad input variables c=%s l=%d r=%d", cartString(cart, "c"), winStart, winEnd); else seqName = hDefaultChrom(database); } struct customTrack *ct = NULL; if (isCustomTrack(track)) { struct customTrack *ctList = getCtList(); for (ct = ctList; ct != NULL; ct = ct->next) if (sameString(track, ct->tdb->track)) break; } if ((!isCustomTrack(track) && dbIsFound) || ((ct!= NULL) && (((ct->dbTrackType != NULL) && sameString(ct->dbTrackType, "maf"))|| sameString(ct->tdb->type, "bigMaf")))) { trackHash = makeTrackHashWithComposites(database, seqName, TRUE); if (sameString("htcBigPslAli", track) || sameString("htcBigPslAliInWindow", track) ) { char *aliTable = cartString(cart, "aliTable"); if (isHubTrack(aliTable)) tdb = hubConnectAddHubForTrackAndFindTdb( database, aliTable, NULL, trackHash); } else if (isHubTrack(track)) { tdb = hubConnectAddHubForTrackAndFindTdb( database, track, NULL, trackHash); } if (parentWigMaf) { int wordCount, i; char *words[16]; char *typeLine; char *wigType = needMem(128); tdb = hashFindVal(trackHash, parentWigMaf); if (!tdb) errAbort("can not find trackDb entry for parentWigMaf track %s.", parentWigMaf); typeLine = cloneString(tdb->type); wordCount = chopLine(typeLine, words); if (wordCount < 1) errAbort("trackDb entry for parentWigMaf track %s has corrupt type line.", parentWigMaf); safef(wigType, 128, "wig "); for (i = 1; i < wordCount; ++i) { strncat(wigType, words[i], 128 - strlen(wigType)); strncat(wigType, " ", 128 - strlen(wigType)); } strncat(wigType, "\n", 128 - strlen(wigType)); tdb->type = wigType; tdb->track = cloneString(track); tdb->table = cloneString(track); freeMem(typeLine); cartRemove(cart, "parentWigMaf"); /* ONE TIME ONLY USE !!! */ } else { tdb = hashFindVal(trackHash, track); if (tdb == NULL) { if (startsWith("all_mrna", track)) tdb = hashFindVal(trackHash, "mrna"); /* Oh what a tangled web we weave. */ } } } char* handler = trackDbSetting(tdb, "trackHandler"); /* Start of 1000+ line dispatch on table involving 100+ if/elses. */ char *table = (tdb ? tdb->table : track); if (sameWord(table, "getDna")) { doGetDna1(); } else if (sameWord(table, "htcGetDna2")) { doGetDna2(); } else if (sameWord(table, "htcGetDna3")) { doGetDna3(); } else if (sameWord(table, "htcGetDnaExtended1")) { doGetDnaExtended1(); } else if (sameWord(table, "buildBigPsl")) { buildBigPsl(item); } else if (sameWord(table, "htcListItemsAssayed")) { doPeakClusterListItemsAssayed(); } /* Lowe Lab Stuff */ #ifdef LOWELAB else if (loweLabClick(table, item, tdb)) { /* do nothing, everything handled in loweLabClick */ } #endif else if (sameWord(table, G_DELETE_WIKI_ITEM)) { doDeleteWikiItem(item, seqName, winStart, winEnd); } else if (sameWord(table, G_ADD_WIKI_COMMENTS)) { doAddWikiComments(item, seqName, winStart, winEnd); } else if (sameWord(table, G_CREATE_WIKI_ITEM)) { doCreateWikiItem(item, seqName, winStart, winEnd); } else if (sameString(track, "variome")) doVariome(item, seqName, winStart, winEnd); else if (sameString(track, "variome.create")) doCreateVariomeItem(item, seqName, winStart, winEnd); else if (sameString(track, "variome.delete")) doDeleteVariomeItem(item, seqName, winStart, winEnd); else if (sameString(track, "variome.addComments")) doAddVariomeComments(item, seqName, winStart, winEnd); else if (startsWith("transMap", table)) transMapClickHandler(tdb, item); else if (startsWith("hgcTransMapCdnaAli", table)) { char *aliTable = cartString(cart, "aliTable"); char *track = hGetTrackForTable(database, aliTable); tdb = hashMustFindVal(trackHash, track); transMapShowCdnaAli(tdb, item); } else if (sameWord(table, "mrna") || sameWord(table, "mrna2") || startsWith("all_mrna",table) || sameWord(table, "all_est") || sameWord(table, "celeraMrna") || sameWord(table, "est") || sameWord(table, "intronEst") || sameWord(table, "xenoMrna") || sameWord(table, "xenoBestMrna") || startsWith("mrnaBlastz",table ) || startsWith("mrnaBad",table ) || sameWord(table, "xenoBlastzMrna") || sameWord(table, "sim4") || sameWord(table, "xenoEst") || sameWord(table, "psu") || sameWord(table, "tightMrna") || sameWord(table, "tightEst") || sameWord(table, "blatzHg17KG") || sameWord(table, "mapHg17KG") ) { doHgRna(tdb, item); } else if (startsWith("pseudoMrna",table ) || startsWith("pseudoGeneLink",table ) || sameWord("pseudoUcsc",table)) { doPseudoPsl(tdb, item); } else if (startsWith("retroMrna",table ) || startsWith("retroAugust",table )|| startsWith("retroCds",table )|| startsWith("ucscRetro",table )) { retroClickHandler(tdb, item); } else if (sameString(table, "hgcRetroCdnaAli")) retroShowCdnaAli(item); else if (sameWord(table, "affyU95") || sameWord(table, "affyU133") || sameWord(table, "affyU74") || sameWord(table, "affyRAE230") || sameWord(table, "affyZebrafish") || sameWord(table, "affyGnf1h") || sameWord(table, "affyMOE430v2") || sameWord(table, "affyGnf1m") ) { doAffy(tdb, item, NULL); } else if (sameWord(table, WIKI_TRACK_TABLE)) doWikiTrack(item, seqName, winStart, winEnd); else if (sameWord(table, OLIGO_MATCH_TRACK_NAME)) doOligoMatch(item); else if (sameWord(table, "refFullAli")) { doTSS(tdb, item); } else if (sameWord(table, "rikenMrna")) { doRikenRna(tdb, item); } else if (sameWord(table, "cgapSage")) { doCgapSage(tdb, item); } else if (sameWord(table, "ctgPos") || sameWord(table, "ctgPos2")) { doHgContig(tdb, item); } else if (sameWord(table, "clonePos")) { doHgCover(tdb, item); } else if (sameWord(table, "bactigPos")) { doBactigPos(tdb, item); } else if (sameWord(table, "hgClone")) { tdb = hashFindVal(trackHash, "clonePos"); doHgClone(tdb, item); } else if (sameWord(table, "gold")) { doHgGold(tdb, item); } else if (sameWord(table, "gap")) { doHgGap(tdb, item); } else if (sameWord(table, "tet_waba")) { doHgTet(tdb, item); } else if (sameWord(table, "wabaCbr")) { doHgCbr(tdb, item); } else if (startsWith("rmskJoined", table)) { doJRepeat(tdb, item); } else if (startsWith("rmsk", table)) { doHgRepeat(tdb, item); } else if (sameWord(table, "isochores")) { doHgIsochore(tdb, item); } else if (sameWord(table, "simpleRepeat")) { doSimpleRepeat(tdb, item); } else if (startsWith("cpgIsland", table)) { doCpgIsland(tdb, item); } else if (sameWord(table, "illuminaProbes")) { doIlluminaProbes(tdb, item); } else if (sameWord(table, "htcIlluminaProbesAlign")) { htcIlluminaProbesAlign(item); } else if (sameWord(table, "switchDbTss")) { doSwitchDbTss(tdb, item); } else if (sameWord(table, "omimLocation")) { doOmimLocation(tdb, item); } else if (sameWord(table, "omimAvSnp")) { doOmimAvSnp(tdb, item); } else if (sameWord(table, "omimGeneClass2")) { doOmimGene2(tdb, item); } else if (sameWord(table, "omimGene2")) { doOmimGene2(tdb, item); } else if (sameWord(table, "omimAv")) { doOmimAv(tdb, item); } else if (sameWord(table, "rgdGene")) { doRgdGene(tdb, item); } else if (sameWord(table, "rgdGene2")) { doRgdGene2(tdb, item); } else if (sameWord(table, "rgdEst")) { doHgRna(tdb, item); } else if (sameWord(table, "rgdSslp")) { doRgdSslp(tdb, item, NULL); } else if (sameWord(table, "gad")) { doGad(tdb, item, NULL); } else if (sameWord(table, "decipher")) { doDecipherCnvs(tdb, item, NULL); } else if (sameWord(table, "decipherSnvs")) { doDecipherSnvs(tdb, item, NULL); } else if (sameWord(table, "omimGene")) { doOmimGene(tdb, item); } else if (sameWord(table, "rgdQtl") || sameWord(table, "rgdRatQtl")) { doRgdQtl(tdb, item); } else if (sameWord(table, "superfamily")) { doSuperfamily(tdb, item, NULL); } else if (sameWord(table, "ensGene") || sameWord (table, "ensGeneNonCoding")) { doEnsemblGene(tdb, item, NULL); } else if (sameWord(table, "xenoRefGene")) { doRefGene(tdb, item); } else if (sameWord(table, "knownGene")) { doKnownGene(tdb, item); } else if (matchTableOrHandler("ncbiRefSeq", tdb) || sameWord(table, "ncbiRefSeqPsl") || sameWord(table, "ncbiRefSeqCurated") || sameWord(table, "ncbiRefSeqPredicted") ) { doNcbiRefSeq(tdb, item); } else if (sameWord(table, "ncbiRefSeqOther") ) { genericClickHandler(tdb, item, NULL); } else if (sameWord(table, "refGene") ) { doRefGene(tdb, item); } else if (sameWord(table, "ccdsGene")) { doCcdsGene(tdb, item); } else if (isNewGencodeGene(tdb)) { doGencodeGene(tdb, item); } else if (sameWord(table, "mappedRefSeq")) /* human refseqs on chimp browser */ { doRefGene(tdb, item); } else if (sameWord(table, "mgcGenes") || sameWord(table, "mgcFullMrna")) { doMgcGenes(tdb, item); } else if (sameWord(table, "orfeomeGenes") || sameWord(table, "orfeomeMrna")) { doOrfeomeGenes(tdb, item); } else if (startsWith("viralProt", table)) { doViralProt(tdb, item); } else if (sameWord("otherSARS", table)) { doPslDetailed(tdb, item); } else if (sameWord(table, "softberryGene")) { doSoftberryPred(tdb, item); } else if (sameWord(table, "borkPseudo")) { doPseudoPred(tdb, item); } else if (sameWord(table, "borkPseudoBig")) { doPseudoPred(tdb, item); } else if (startsWith("encodePseudogene", table)) { doEncodePseudoPred(tdb,item); } else if (sameWord(table, "sanger22")) { doSangerGene(tdb, item, "sanger22pep", "sanger22mrna", "sanger22extra"); } else if (sameWord(table,"tRNAs")) { doTrnaGenesGb(tdb, item); } else if (sameWord(table, "sanger20")) { doSangerGene(tdb, item, "sanger20pep", "sanger20mrna", "sanger20extra"); } else if (sameWord(table, "vegaGene") || sameWord(table, "vegaPseudoGene") ) { doVegaGene(tdb, item, NULL); } else if ((sameWord(table, "vegaGene") || sameWord(table, "vegaPseudoGene")) && hTableExists(database, "vegaInfoZfish")) { doVegaGeneZfish(tdb, item); } else if (sameWord(table, "genomicDups")) { doGenomicDups(tdb, item); } else if (sameWord(table, "blatMouse") || sameWord(table, "bestMouse") || sameWord(table, "blastzTest") || sameWord(table, "blastzTest2")) { doBlatMouse(tdb, item); } else if (startsWith("multAlignWebb", table)) { doMultAlignZoo(tdb, item, &table[13] ); } else if (sameWord(table, "exaptedRepeats")) { doExaptedRepeats(tdb, item); } /* Generalized code to show strict chain blastz alignments in the zoo browsers */ else if (containsStringNoCase(table, "blastzStrictChain") && containsStringNoCase(database, "zoo")) { int len = strlen("blastzStrictChain"); char *orgName = &table[len]; char dbName[32] = "zoo"; strcpy(&dbName[3], orgName); len = strlen(orgName); strcpy(&dbName[3 + len], "3"); longXenoPsl1(tdb, item, orgName, "chromInfo", dbName); } else if (sameWord(table, "blatChimp") || sameWord(table, "chimpBac") || sameWord(table, "bacChimp")) { longXenoPsl1Chimp(tdb, item, "Chimpanzee", "chromInfo", database); } else if (sameWord(table, "htcLongXenoPsl2")) { htcLongXenoPsl2(table, item); } else if (sameWord(table, "htcCdnaAliInWindow")) { htcCdnaAliInWindow(item); } else if (sameWord(table, "htcPseudoGene")) { htcPseudoGene(table, item); } else if (sameWord(table, "tfbsConsSites")) { tfbsConsSites(tdb, item); } else if (sameWord(table, "tfbsCons")) { tfbsCons(tdb, item); } else if (startsWith("atom", table) && !startsWith("atomMaf", table)) { doAtom(tdb, item); } else if (sameWord(table, "firstEF")) { firstEF(tdb, item); } else if ( sameWord(table, "blastHg16KG") || sameWord(table, "blatHg16KG" ) || startsWith("blastDm", table) || sameWord(table, "blastMm6KG") || sameWord(table, "blastSacCer1SG") || sameWord(table, "blastHg17KG") || startsWith("blastCe", table) || sameWord(table, "blastHg18KG") ) { blastProtein(tdb, item); } else if (startsWith("altSeqLiftOverPsl", table) || startsWith("fixSeqLiftOverPsl", table)) { doPslAltSeq(tdb, item); } else if (sameWord(table, "chimpSimpleDiff")) { doSimpleDiff(tdb, "Chimp"); } /* This is a catch-all for blastz/blat tracks -- any special cases must be * above this point! */ else if (startsWith("map", table) ||startsWith("blastz", table) || startsWith("blat", table) || startsWith("tblast", table) || endsWith(table, "Blastz")) { char *genome = "Unknown"; if (startsWith("tblast", table)) genome = &table[6]; if (startsWith("map", table)) genome = &table[3]; if (startsWith("blat", table)) genome = &table[4]; if (startsWith("blastz", table)) genome = &table[6]; else if (endsWith(table,"Blastz")) { genome = table; *strstr(genome, "Blastz") = 0; } if (hDbExists(genome)) { /* handle table that include other database name * in trackname; e.g. blatCe1, blatCb1, blatCi1, blatHg15, blatMm3... * Uses genome column from database table as display text */ genome = hGenome(genome); } doAlignCompGeno(tdb, item, genome); } else if (sameWord(table, "rnaGene")) { doRnaGene(tdb, item); } else if (startsWith("rnaStruct", table) || sameWord(table, "RfamSeedFolds") || sameWord(table, "RfamFullFolds") || sameWord(table, "rfamTestFolds") || sameWord(table, "evofold") || sameWord(table, "evofoldV2") || sameWord(table, "evofoldRaw") || sameWord(table, "encode_tba23EvoFold") || sameWord(table, "encodeEvoFold") || sameWord(table, "rnafold") || sameWord(table, "rnaTestFolds") || sameWord(table, "rnaTestFoldsV2") || sameWord(table, "rnaTestFoldsV3") || sameWord(table, "mcFolds") || sameWord(table, "rnaEditFolds") || sameWord(table, "altSpliceFolds") || stringIn(table, "rnaSecStr")) { doRnaSecStr(tdb, item); } else if (sameWord(table, "fishClones")) { doFishClones(tdb, item); } else if (sameWord(table, "stsMarker")) { doStsMarker(tdb, item); } else if (sameWord(table, "stsMapMouse")) { doStsMapMouse(tdb, item); } else if (sameWord(table, "stsMapMouseNew")) /*steal map rat code for new mouse sts table. */ { doStsMapMouseNew(tdb, item); } else if(sameWord(table, "stsMapRat")) { doStsMapRat(tdb, item); } else if (sameWord(table, "stsMap")) { doStsMarker(tdb, item); } else if (sameWord(table, "rhMap")) { doZfishRHmap(tdb, item); } else if (sameWord(table, "yaleBertoneTars")) { doYaleTars(tdb, item, NULL); } else if (sameWord(table, "recombRate")) { doRecombRate(tdb); } else if (sameWord(table, "recombRateRat")) { doRecombRateRat(tdb); } else if (sameWord(table, "recombRateMouse")) { doRecombRateMouse(tdb); } else if (sameWord(table, "genMapDb")) { doGenMapDb(tdb, item); } else if (sameWord(table, "mouseSynWhd")) { doMouseSynWhd(tdb, item); } else if (sameWord(table, "ensRatMusHom")) { doEnsPhusionBlast(tdb, item); } else if (sameWord(table, "mouseSyn")) { doMouseSyn(tdb, item); } else if (sameWord(table, "mouseOrtho")) { doMouseOrtho(tdb, item); } else if (sameWord(table, USER_PSL_TRACK_NAME)) { doUserPsl(table, item); } else if (sameWord(table, PCR_RESULT_TRACK_NAME)) { doPcrResult(table, item); } else if (sameWord(table, "softPromoter")) { hgSoftPromoter(table, item); } else if (isCustomTrack(table)) { if (tdb != NULL) { char *origTrackName = trackDbSetting(tdb, "origTrackName"); if (origTrackName) table = origTrackName; } hgCustom(table, item); } else if (sameWord(table, "snpTsc") || sameWord(table, "snpNih") || sameWord(table, "snpMap")) { doSnpOld(tdb, item); } else if (sameWord(table, "snp")) { doSnp(tdb, item); } else if (snpVersion(table) >= 125) { doSnpWithVersion(tdb, item, snpVersion(table)); } else if (sameWord(table, "cnpIafrate")) { doCnpIafrate(tdb, item); } else if (sameWord(table, "cnpLocke")) { doCnpLocke(tdb, item); } else if (sameWord(table, "cnpIafrate2")) { doCnpIafrate2(tdb, item); } else if (sameWord(table, "cnpSebat")) { doCnpSebat(tdb, item); } else if (sameWord(table, "cnpSebat2")) { doCnpSebat2(tdb, item); } else if (sameWord(table, "cnpSharp")) { doCnpSharp(tdb, item); } else if (sameWord(table, "cnpSharp2")) { doCnpSharp2(tdb, item); } else if (sameWord(table, "delHinds2")) { doDelHinds2(tdb, item); } else if (sameWord(table, "delConrad2")) { doDelConrad2(tdb, item); } else if (sameWord(table, "dgv") || sameWord(table, "dgvBeta")) { doDgv(tdb, item); } else if (sameWord(table, "dgvMerged") || sameWord(table, "dgvSupporting")) { doDgvPlus(tdb, item); } else if (sameWord(table, "affy120K")) { doAffy120K(tdb, item); } else if (sameWord(table, "affy10K")) { doAffy10K(tdb, item); } else if (sameWord(table, "uniGene_2") || sameWord(table, "uniGene")) { doSageDataDisp(table, item, tdb); } else if (sameWord(table, "uniGene_3")) { doUniGene3(tdb, item); } else if (sameWord(table, "vax003") || sameWord(table, "vax004")) { doVax003Vax004(tdb, item); } else if (sameWord(table, "tigrGeneIndex")) { doTigrGeneIndex(tdb, item); } //else if ((sameWord(table, "bacEndPairs")) || (sameWord(table, "bacEndPairsBad")) || (sameWord(table, "bacEndPairsLong")) || (sameWord(table, "bacEndSingles"))) //{ //doLinkedFeaturesSeries(table, item, tdb); //} else if (sameAltWords(table, handler, "bacEndPairs", "bacEndPairsBad", "bacEndPairsLong", "bacEndSingles", NULL)) { doLinkedFeaturesSeries(table, item, tdb); } else if ((sameWord(table, "fosEndPairs")) || (sameWord(table, "fosEndPairsBad")) || (sameWord(table, "fosEndPairsLong"))) { doLinkedFeaturesSeries(table, item, tdb); } else if ((sameWord(table, "earlyRep")) || (sameWord(table, "earlyRepBad"))) { doLinkedFeaturesSeries(table, item, tdb); } else if (sameWord(table, "cgh")) { doCgh(table, item, tdb); } else if (sameWord(table, "mcnBreakpoints")) { doMcnBreakpoints(table, item, tdb); } else if (sameWord(table, "htcChainAli")) { htcChainAli(item); } else if (sameWord(table, "htcChainTransAli")) { htcChainTransAli(item); } else if (sameWord(table, "htcBigPslAliInWindow")) { htcBigPslAliInWindow(item); } else if (sameWord(table, "htcBigPslAli")) { htcBigPslAli(item); } else if (sameWord(table, "htcCdnaAli")) { htcCdnaAli(item); } else if (sameWord(table, "htcUserAli")) { htcUserAli(item); } else if (sameWord(table, "htcGetBlastPep")) { doGetBlastPep(item, cartString(cart, "aliTable")); } else if (sameWord(table, "htcProteinAli")) { htcProteinAli(item, cartString(cart, "aliTable")); } else if (sameWord(table, "htcBlatXeno")) { htcBlatXeno(item, cartString(cart, "aliTable")); } else if (sameWord(table, "htcExtSeq")) { htcExtSeq(item); } else if (sameWord(table, "htcTranslatedProtein")) { htcTranslatedProtein(item); } else if (sameWord(table, "htcTranslatedPredMRna")) { htcTranslatedPredMRna(item); } else if (sameWord(table, "htcTranslatedMRna")) { htcTranslatedMRna(tdbForTableArg(), item); } else if (sameWord(table, "ncbiRefSeqSequence")) { ncbiRefSeqSequence(item); } else if (sameWord(table, "htcGeneMrna")) { htcGeneMrna(item); } else if (sameWord(table, "htcRefMrna")) { htcRefMrna(item); } else if (sameWord(table, "htcDisplayMrna")) { htcDisplayMrna(item); } else if (sameWord(table, "htcGeneInGenome")) { htcGeneInGenome(item); } else if (sameWord(table, "htcDnaNearGene")) { htcDnaNearGene( item); } else if (sameWord(table, "getMsBedAll")) { getMsBedExpDetails(tdb, item, TRUE); } else if (sameWord(table, "getMsBedRange")) { getMsBedExpDetails(tdb, item, FALSE); } else if (sameWord(table, "perlegen")) { perlegenDetails(tdb, item); } else if (sameWord(table, "haplotype")) { haplotypeDetails(tdb, item); } else if (sameWord(table, "mitoSnps")) { mitoDetails(tdb, item); } else if (sameWord(table, "loweProbes")) { doProbeDetails(tdb, item); } else if (sameWord(table, "chicken13k")) { doChicken13kDetails(tdb, item); } else if( sameWord(table, "ancientR")) { ancientRDetails(tdb, item); } else if( sameWord(table, "gcPercent")) { doGcDetails(tdb, item); } else if (sameWord(table, "htcTrackHtml")) { htcTrackHtml(tdbForTableArg()); } /*Evan's stuff*/ else if (sameWord(table, "genomicSuperDups")) { doGenomicSuperDups(tdb, item); } else if (sameWord(table, "celeraDupPositive")) { doCeleraDupPositive(tdb, item); } else if (sameWord(table, "triangle") || sameWord(table, "triangleSelf") || sameWord(table, "transfacHit") ) { doTriangle(tdb, item, "dnaMotif"); } else if (sameWord(table, "esRegGeneToMotif")) { doTriangle(tdb, item, "esRegMotif"); } else if (startsWith("wgEncodeRegTfbsClusteredMotifs", table)) { doTriangle(tdb, item, "transRegCodeMotif"); } else if (sameWord(table, "transRegCode")) { doTransRegCode(tdb, item, "transRegCodeMotif"); } else if (sameWord(table, "transRegCodeProbe")) { doTransRegCodeProbe(tdb, item, "transRegCode", "transRegCodeMotif", "transRegCodeCondition", "growthCondition"); } else if (tdb != NULL && startsWith("wgEncodeRegDnaseClustered", tdb->track)) { doPeakClusters(tdb, item); } else if( sameWord( table, "humMusL" ) || sameWord( table, "regpotent" )) { humMusClickHandler( tdb, item, "Mouse", "mm2", "blastzBestMouse", 0); } else if( sameWord( table, "musHumL" )) { humMusClickHandler( tdb, item, "Human", "hg12", "blastzBestHuman_08_30" , 0); } else if( sameWord( table, "mm3Rn2L" )) { humMusClickHandler( tdb, item, "Rat", "rn2", "blastzBestRat", 0 ); } else if( sameWord( table, "hg15Mm3L" )) { humMusClickHandler( tdb, item, "Mouse", "mm3", "blastzBestMm3", 0 ); } else if( sameWord( table, "mm3Hg15L" )) { humMusClickHandler( tdb, item, "Human", "hg15", "blastzNetHuman" , 0); } else if( sameWord( table, "footPrinter" )) { footPrinterClickHandler( tdb, item ); } else if (sameWord(table, "jaxQTL3")) { doJaxQTL3(tdb, item); } else if (startsWith("jaxQTL", table) || startsWith("jaxQtl", table)) { doJaxQTL(tdb, item); } else if (startsWith("jaxAllele", table) || startsWith("jaxGeneTrap", table)) { doJaxAllele(tdb, item); } else if (startsWith("jaxPhenotype", table)) { doJaxPhenotype(tdb, item); } else if (startsWith("jaxRepTranscript", table)) { doJaxAliasGenePred(tdb, item); } else if (sameWord(table, "wgRna")) { doWgRna(tdb, item); } else if (sameWord(table, "ncRna")) { doNcRna(tdb, item); } else if (sameWord(table, "gbProtAnn")) { doGbProtAnn(tdb, item); } else if (sameWord(table, "bdgpGene") || sameWord(table, "bdgpNonCoding")) { doBDGPGene(tdb, item); } else if (sameWord(table, "flyBaseGene") || sameWord(table, "flyBaseNoncoding")) { doFlyBaseGene(tdb, item); } else if (sameWord(table, "bgiGene")) { doBGIGene(tdb, item); } else if (sameWord(table, "bgiSnp")) { doBGISnp(tdb, item); } else if (sameWord(table, "encodeRna")) { doEncodeRna(tdb, item); } else if (sameWord(table, "encodeRegions")) { doEncodeRegion(tdb, item); } else if (sameWord(table, "encodeErgeHssCellLines")) { doEncodeErgeHssCellLines(tdb, item); } else if (sameWord(table, "encodeErge5race") || sameWord(table, "encodeErgeInVitroFoot") || \ sameWord(table, "encodeErgeDNAseI") || sameWord(table, "encodeErgeMethProm") || \ sameWord(table, "encodeErgeExpProm") || sameWord(table, "encodeErgeStableTransf") || \ sameWord(table, "encodeErgeBinding") || sameWord(table, "encodeErgeTransTransf") || \ sameWord(table, "encodeErgeSummary")) { doEncodeErge(tdb, item); } else if(sameWord(table, "HInvGeneMrna")) { doHInvGenes(tdb, item); } else if(sameWord(table, "sgdClone")) { doSgdClone(tdb, item); } else if (sameWord(table, "sgdOther")) { doSgdOther(tdb, item); } else if (sameWord(table, "vntr")) { doVntr(tdb, item); } else if (sameWord(table, "luNega") || sameWord (table, "luPosi") || sameWord (table, "mRNARemains") || sameWord(table, "pseudoUcsc2")) { doPutaFrag(tdb, item); } else if (sameWord(table, "potentPsl") || sameWord(table, "rcntPsl") ) { potentPslAlign(table, item); } else if (startsWith("zdobnov", table)) { doZdobnovSynt(tdb, item); } else if (startsWith("deweySynt", table)) { doDeweySynt(tdb, item); } else if (startsWith("eponine", table)) { doBed6FloatScore(tdb, item); printTrackHtml(tdb); } else if (sameWord(organism, "fugu") && startsWith("ecores", table)) { doScaffoldEcores(tdb, item); } else if (startsWith("pscreen", table)) { doPscreen(tdb, item); } else if (startsWith("flyreg", table)) { doFlyreg(tdb, item); } /* ENCODE table */ else if (startsWith("encodeGencodeIntron", table) && sameString(tdb->type, "bed 6 +")) { doGencodeIntron(tdb, item); } else if (sameWord(table, "encodeIndels")) { doEncodeIndels(tdb, item); } else if (startsWith("encodeStanfordPromoters", table)) { doEncodeStanfordPromoters(tdb, item); } else if (startsWith("encodeStanfordRtPcr", table)) { doEncodeStanfordRtPcr(tdb, item); } else if (startsWith("encodeHapMapAlleleFreq", table)) { doEncodeHapMapAlleleFreq(tdb, item); } else if (sameString("cutters", table)) { doCutters(item); } else if (sameString("anoEstTcl", table)) { doAnoEstTcl(tdb, item); } else if (sameString("interPro", table)) { doInterPro(tdb, item); } else if (sameString("dvBed", table)) { doDv(tdb, item); } else if (startsWith("hapmapSnps", table) && (strlen(table) == 13 || (endsWith(table, "PhaseII") && strlen(table) == 20))) { doHapmapSnps(tdb, item); } else if (startsWith("hapmapAllelesChimp", table) || startsWith("hapmapAllelesMacaque", table)) { doHapmapOrthos(tdb, item); } else if (sameString("snpArrayAffy250Nsp", table) || sameString("snpArrayAffy250Sty", table) || sameString("snpArrayAffy5", table) || sameString("snpArrayAffy6", table) || sameString("snpArrayAffy10", table) || sameString("snpArrayAffy10v2", table) || sameString("snpArrayAffy50HindIII", table) || sameString("snpArrayAffy50XbaI", table)) { doSnpArray(tdb, item, "Affy"); } else if (sameString("snpArrayIllumina300", table) || sameString("snpArrayIllumina550", table) || sameString("snpArrayIllumina650", table) || (sameString("snpArrayIllumina1M", table) && startsWith("rs", item) ) || (sameString("snpArrayIlluminaHuman660W_Quad", table) && startsWith("rs", item) ) || (sameString("snpArrayIlluminaHumanOmni1_Quad", table) && startsWith("rs", item) ) || (sameString("snpArrayIlluminaHumanCytoSNP_12", table) && startsWith("rs", item) ) ) { doSnpArray(tdb, item, "Illumina"); } else if ( (sameString("snpArrayIlluminaHuman660W_Quad", table) && !startsWith("rs", item) ) || (sameString("snpArrayIlluminaHumanOmni1_Quad", table) && !startsWith("rs", item) ) || (sameString("snpArrayIlluminaHumanCytoSNP_12", table) && !startsWith("rs", item) ) ) { /* special processing for non-dbSnp entries of the 3 new Illumina arrays */ doSnpArray2(tdb, item, "Illumina"); } else if (sameString("pgVenter", table) || sameString("pgWatson", table) || sameString("pgYri", table) || sameString("pgCeu", table) || sameString("pgChb", table) || sameString("pgJpt", table) || sameString("pgSjk", table) || startsWith("pgYoruban", table) || (startsWith("pgNA", table) && isdigit(table[4])) || sameString("hbPgTest", table) || sameString("hbPgWild", table) || sameString("pgYh1", table) || sameString("pgKb1", table) || sameString("pgNb1", table) || sameString("pgNb1Indel", table) || sameString("pgTk1", table) || sameString("pgTk1Indel", table) || sameString("pgMd8", table) || sameString("pgMd8Indel", table) || sameString("pgKb1Illum", table) || sameString("pgKb1454", table) || sameString("pgKb1Indel", table) || sameString("pgKb1Comb", table) || sameString("pgAbtSolid", table) || sameString("pgAbt", table) || sameString("pgAbt454", table) || sameString("pgAbt454indels", table) || sameString("pgAbtIllum", table) || sameString("pgAk1", table) || sameString("pgQuake", table) || sameString("pgIrish", table) || sameString("pgSaqqaq", table) || sameString("pgSaqqaqHc", table) || sameString("pgTest", table) ) { doPgSnp(tdb, item, NULL); } else if (startsWith("pg", table) && (endsWith(table, "PhenCode") || endsWith(table, "Snpedia") || endsWith(table, "Hgmd")) ) { doPgPhenoAssoc(tdb, item); } else if (sameString("gvPos", table)) { doGv(tdb, item); } else if (sameString("protVarPos", table)) { doProtVar(tdb, item); } else if (sameString("oreganno", table)) { doOreganno(tdb, item); } else if (sameString("oregannoOther", table)) { /* Regions from another species lifted and displayed in current */ /* same table structure, just different table name/table */ doOreganno(tdb, item); } else if (sameString("allenBrainAli", table)) { doAllenBrain(tdb, item); } else if (sameString("dless", table) || sameString("encodeDless", table)) { doDless(tdb, item); } else if (sameString("mammalPsg", table)) { doMammalPsg(tdb, item); } else if (sameString("igtc", table)) { doIgtc(tdb, item); } else if (sameString("rdmr", table)) { doRdmr(tdb, item); } else if (startsWith("komp", table) || startsWith("ikmc", table)) { doKomp(tdb, item); } else if (sameString("hgIkmc", table)) { doHgIkmc(tdb, item); } else if (startsWith("dbRIP", table)) { dbRIP(tdb, item, NULL); } else if (sameString("omicia", table)) //Auto", table) || sameString("omiciaHand", table)) { doOmicia(tdb, item); } else if ( sameString("expRatioUCSFDemo", table) || sameString("cnvLungBroadv2", table) || sameString("CGHBreastCancerUCSF", table) || sameString("expBreastCancerUCSF", table)) { doUCSFDemo(tdb, item); } else if (startsWith("consIndels", table)) { doConsIndels(tdb,item); } else if (startsWith(KIDD_EICHLER_DISC_PREFIX, table)) { doKiddEichlerDisc(tdb, item); } else if (startsWith("hgdpGeo", table)) { doHgdpGeo(tdb, item); } else if (startsWith("gwasCatalog", table)) { doGwasCatalog(tdb, item); } else if (sameString("par", table)) { doParDetails(tdb, item); } else if (startsWith("pubs", table)) { doPubsDetails(tdb, item); } else if (tdb != NULL && startsWith("bedDetail", tdb->type)) { doBedDetail(tdb, NULL, item); } else if (startsWith("numtS", table)) { doNumtS(tdb, item); } else if (sameString("cosmic", table)) { doCosmic(tdb, item); } else if (sameString("geneReviews", table)) { doGeneReviews(tdb, item); } else if (startsWith("qPcrPrimers", table)) { doQPCRPrimers(tdb, item); } else if (sameString("lrg", table)) { doLrg(tdb, item); } else if (sameString("lrgTranscriptAli", table)) { doLrgTranscriptPsl(tdb, item); } else if (sameWord(table, "htcLrgCdna")) { htcLrgCdna(item); } else if (startsWith("peptideAtlas", table)) { doPeptideAtlas(tdb, item); } else if (startsWith("gtexGene", table)) { doGtexGeneExpr(tdb, item); } else if (startsWith("gtexEqtlCluster", table)) { doGtexEqtlDetails(tdb, item); } else if (startsWith("snake", trackHubSkipHubName(table))) { doSnakeClick(tdb, item); } else if (tdb != NULL && (startsWithWord("vcfTabix", tdb->type) || sameWord("vcfPhasedTrio", tdb->type))) { doVcfTabixDetails(tdb, item); } else if (tdb != NULL && startsWithWord("vcf", tdb->type)) { doVcfDetails(tdb, item); } else if (tdb != NULL && (startsWithWord("barChart", tdb->type) || startsWithWord("bigBarChart", tdb->type))) { doBarChartDetails(tdb, item); printTrackHtml(tdb); } else if (tdb != NULL) { genericClickHandler(tdb, item, NULL); } else { cartWebStart(cart, database, "%s", track); warn("Sorry, clicking there doesn't do anything yet (%s).", track); } /* End of 1000+ line dispatch on table involving 100+ if/elses. */ cartHtmlEnd(); } struct hash *orgDbHash = NULL; void initOrgDbHash() /* Function to initialize a hash of organism names that hash to a database ID. * This is used to show alignments by hashing the organism associated with the * track to the database name where the chromInfo is stored. For example, the * mousBlat track in the human browser would hash to the mm2 database. */ { orgDbHash = hashNew(8); } void cartDoMiddle(struct cart *theCart) /* Save cart and do main middle handler. */ { initOrgDbHash(); cart = theCart; doMiddle(); } char *excludeVars[] = {"Submit", "submit", "g", "i", "aliTable", "addp", "pred", NULL}; int main(int argc, char *argv[]) { long enteredMainTime = clock1000(); pushCarefulMemHandler(LIMIT_2or6GB); cgiSpoof(&argc,argv); cartEmptyShell(cartDoMiddle, hUserCookie(), excludeVars, NULL); cgiExitTime("hgc", enteredMainTime); return 0; }