a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c galt Mon Jan 30 16:18:41 2017 -0800 Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c. diff --git src/hg/hgc/lowelab.c src/hg/hgc/lowelab.c index a367911..b51326a 100644 --- src/hg/hgc/lowelab.c +++ src/hg/hgc/lowelab.c @@ -1,3918 +1,3918 @@ /* Lowe Lab additions for Archaea and Bacterial details pages*/ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "obscure.h" #include "hCommon.h" #include "hash.h" #include "bits.h" #include "memgfx.h" #include "portable.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 "xenalign.h" #include "isochores.h" #include "genePred.h" #include "genePredReader.h" #include "pepPred.h" #include "wabAli.h" #include "minGeneInfo.h" #include "rnaGene.h" #include "tRNAs.h" #include "snoRNAs.h" #include "gbRNAs.h" #include "hgMaf.h" #include "maf.h" #include "hgConfig.h" #include "web.h" #include "dbDb.h" #include "sample.h" #include "axt.h" #include "gbProtAnn.h" #include "hgSeq.h" #include "chain.h" #include "chainNet.h" #include "chainDb.h" #include "chainToPsl.h" #include "chainToAxt.h" #include "netAlign.h" #include "tigrCmrGene.h" #include "jgiGene.h" #include "lowelabPfamHit.h" #include "lowelabArkinOperonScore.h" #include "lowelabTIGROperonScore.h" #include "sargassoSeaXra.h" #include "codeBlastScore.h" #include "codeBlast.h" #include "tigrOperon.h" #include "easyGene.h" #include "llaInfo.h" #include "blastTab.h" #include "hdb.h" #include "hgc.h" #include "genbank.h" #include "pseudoGeneLink.h" #include "axtLib.h" #include "tfbsCons.h" #include "tfbsConsMap.h" #include "tfbsConsSites.h" #include "tfbsConsFactors.h" #include "simpleNucDiff.h" #include "botDelay.h" #include "bed5FloatScore.h" #include "bed6FloatScore.h" #include "pscreen.h" #include "gapCalc.h" #include "chainConnect.h" #include "ec.h" #include "transMapClick.h" #include "ccdsClick.h" #include "memalloc.h" #include "rnaHybridization.h" #include "cddInfo.h" #include "alignInfo.h" #include "loweutils.h" #include "cddDesc.h" #include "arCOGs.h" #include "arcogdesc.h" #include "megablastInfo.h" #include "geneTree.h" /*#define LISTUI*/ extern char *uniprotFormat; static void goPrint( struct sqlConnection *conn, char *geneId, char *acc) /* Print out GO annotations. */ { struct sqlConnection *goConn = sqlConnect("go"); char query[512]; struct sqlResult *sr; char **row; static char *aspects[3] = {"F", "P", "C"}; static char *aspectNames[3] = { "Molecular Function", "Biological Process", "Cellular Component", }; int aspectIx; int termCount = 0; if (sqlTableExists(goConn,"goaPart") && sqlTableExists(goConn,"term")) for (aspectIx = 0; aspectIx < ArraySize(aspects); ++aspectIx) { boolean hasFirst = FALSE; sqlSafef(query, sizeof(query), "select term.acc,term.name" " from goaPart,term" " where goaPart.dbObjectId = '%s'" " and goaPart.goId = term.acc" " and goaPart.aspect = '%s'" , acc, aspects[aspectIx]); sr = sqlGetResult(goConn, query); while ((row = sqlNextRow(sr)) != NULL) { char *goID = row[0]; char *goTermName = row[1]; if (!hasFirst) { printf("<B>%s:</B><BR>", aspectNames[aspectIx]); hasFirst = TRUE; } printf("<A HREF = \""); printf("http://godatabase.org/cgi-bin/go.cgi?view=details&depth=1&query=%s", goID); printf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName); termCount++; } if (hasFirst) printf("<BR>"); sqlFreeResult(&sr); } if (termCount == 0) printf("Not available<BR>\n"); sqlDisconnect(&goConn); } void keggOtherGenes(struct sqlConnection *conn, char *geneId, char *table, char *mapId) /* Print out genes linked to a kegg pathway mapId. */ { char query[512], **row; struct sqlResult *sr; char *extraTable = "gbProtCodeXra"; char *keggTable = "keggPathway"; if (hTableExists(database, extraTable)) { sqlSafef(query, sizeof(query), "select x.name, x.gene, x.product from %s k1, %s x " "where k1.mapID = '%s' and " "k1.kgID = x.name ;" , keggTable, extraTable, mapId ); sr = sqlGetResult(conn, query); printf("<table>\n"); while ((row = sqlNextRow(sr)) != NULL) { printf("<tr><td>"); hgcAnchorPosition(table,row[0]); printf("%s</A> <BR>\n",row[0]); if (differentString(row[0],row[1]) && differentString(row[1], "none")) printf("</td><td>%s</td><td>%s</td></tr>\n", row[1], row[2]); else printf("</td><td> </td><td>%s</td></tr>\n", row[2]); } sqlFreeResult(&sr); printf("</table>\n"); } } void keggLink(struct sqlConnection *conn, char *geneId, char *table, char *title) /* Print out kegg database link. */ { char query[512], **row; struct sqlResult *sr; struct sqlConnection *conn2 = hAllocConn(database); sqlSafef(query, sizeof(query), "select keggPathway.locusID,keggPathway.mapID,keggMapDesc.description" " from keggPathway,keggMapDesc" " where keggPathway.kgID='%s'" " and keggPathway.mapID = keggMapDesc.mapID" , geneId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("%s",title); printf("<A HREF=\"http://www.genome.ad.jp/dbget-bin/show_pathway?%s+%s\" TARGET=_blank>", row[1], row[0]); printf("%s</A> - %s<BR>", row[1], row[2]); printf("<B>Other Genes in Kegg Pathway: </b><BR>"); keggOtherGenes(conn2, geneId, table, row[1]); printf("<BR>\n"); } sqlFreeResult(&sr); } int keggCount(struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[256]; char *keggTable = "keggPathway"; if (!hTableExists(database, keggTable)) return 0; sqlSafef(query, sizeof(query), "select count(*) from %s where kgID='%s'", keggTable, geneId); return sqlQuickNum(conn, query); } void modBaseAnchor(char *swissProtAcc) /* Print out anchor to modBase. */ { printf("<A HREF=\"http://salilab.org/modbase-cgi/model_search.cgi?searchkw=name&kword=%s\" TARGET=_blank>", swissProtAcc); } float computeGCContent(char* dna, int length) { float percent = 0.0f; int count = 0; int i = 0; for (i = 0; i < length; i++) { if ((dna[i] == 'C') || (dna[i] == 'c') || (dna[i] == 'G') || (dna[i] == 'g')) count++; } percent = (float) count / (float) length * 100.0f; return percent; } int selfBlastpHitCount(struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[512]; char *blastpHitsTable = "blastpHits"; if (!hTableExists(database, blastpHitsTable)) return 0; sqlSafef(query, sizeof(query), "select count(*) from %s where query = '%s' and target like '%s:%%' and target != '%s:%s'", blastpHitsTable, geneId, database, database, geneId); return sqlQuickNum(conn, query); } struct blastTab* loadSelfBlastpHits(struct sqlConnection *conn, char* queryName, int self) /* Load all blastp hits in the same genome of the given query gene into a list */ { char query[512]; struct sqlResult *srBlastpHits = NULL; struct blastTab *list = NULL; struct blastTab *blastpHits; char **row; char blastpHitsTable[] = "blastpHits"; if (hTableExists(database, blastpHitsTable)) { if (self) { sqlSafef(query, sizeof query, "select * from %s where query = '%s' and target like '%s:%%'", blastpHitsTable, queryName, database); } else { sqlSafef(query, sizeof query, "select * from %s where query = '%s' and target like '%s:%%' and target != '%s:%s'", blastpHitsTable, queryName, database, database, queryName); } srBlastpHits = sqlGetResult(conn, query); while ((row = sqlNextRow(srBlastpHits)) != NULL) { blastpHits = blastTabLoad(row); slAddTail(&list, blastpHits); } } if (srBlastpHits != NULL) sqlFreeResult(&srBlastpHits); return list; } void printSelfHomologs(struct sqlConnection *conn, struct blastTab *blastpHitsList) /* Print self homologs in refseq */ { char query[512]; struct sqlResult *sr; char **row; char refSeq[50]; char xraTable[50]; char product[255]; struct blastTab *blastpHits; struct minGeneInfo *ginfo; char *blastpTarget[2]; char **buffer = NULL; boolean findTable = FALSE; unsigned int cdsStart = 0; unsigned int cdsEnd = 0; printf("<br>\n"); printf("<b>Homologs within genome</b><BR>\n"); /* Print table */ printf("<table style='width:60%%; background-color:#%s;' border=0 cellpadding=1 cellspacing=0>", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 " "cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"20%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"30%%\"><b>BlastP E-value</b></td>\n"); printf("</tr>\n"); blastpHits = blastpHitsList; while (blastpHits != NULL) { parseDelimitedString(blastpHits->target, ':', blastpTarget, 2); if (hTableExists(blastpTarget[0], "lookup")) { sqlSafef(query, sizeof query, "select lookupValue from %s.lookup where lookupCode = 'annotRev'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(refSeq, row[0]); findTable = TRUE; sqlFreeResult(&sr); } } else if (hTableExists(blastpTarget[0], "refSeq")) { strcpy(refSeq, "refSeq"); findTable = TRUE; } if (findTable) { sqlSafef(query, sizeof query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'", refSeq, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { cdsStart = strtoul(row[1], buffer, 10); cdsEnd = strtoul(row[2], buffer, 10); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td><a href=\"hgTracks\?position=%s:%u-%u&db=%s\" TARGET=_blank>%s</a></td>\n", row[0], cdsStart, cdsEnd, blastpTarget[0], blastpTarget[1]); } else printf("<td>%s</td>\n", blastpTarget[1]); sqlFreeResult(&sr); } else printf("<td>%s</td>\n", blastpTarget[1]); if (hTableExists(blastpTarget[0], "lookup")) { sqlSafef(query, sizeof query, "select lookupValue from %s.lookup where lookupCode = 'annotRevXra'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(xraTable, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); sqlSafef(query, sizeof query, "select product from %s where name = '%s'", xraTable, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(product, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); } else { ginfo = getGbProtCodeInfo(conn, blastpTarget[0], blastpTarget[1]); if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none")) strcpy(product, ginfo->product); else strcpy(product, "N/A"); } printf("<td>%s</td>\n", product); printf("<td style=\"text-align: right;\">%0.0e</td>\n", blastpHits->eValue); printf("</tr>\n"); free(blastpTarget[0]); free(blastpTarget[1]); blastpHits = blastpHits->next; } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } int getGeneTree(struct sqlConnection *conn, char *geneId, char *treeFileName) { int success = 0; char query[256]; char *geneTreeTable = "geneTree"; struct sqlResult *sr; char **row; struct geneTree *genetree; if (!hTableExists(database, geneTreeTable)) return 0; sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", geneTreeTable, geneId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { genetree = geneTreeLoad(row); if (!fileExists(treeFileName)) { FILE *f; f = fopen(treeFileName, "w"); if (f != NULL) { fprintf(f, "%s\n", genetree->tree); fclose(f); success = 1; } } else success = 1; } sqlFreeResult(&sr); geneTreeFree(&genetree); return success; } void doRefSeq(struct trackDb *tdb, char *item, char *pepTable, char *extraTable) /* Handle click on gene track. */ { struct minGeneInfo ginfo; char query[256]; char query2[256]; char *gi = NULL; struct sqlResult *sr, *sr2; struct dnaSeq *sequence; char **row, **row2; char *words[16], *dupe = cloneString(tdb->type); int wordCount, x, length; int num = 0; int hits = 0; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2; struct sqlConnection *spConn = NULL; struct COG *COG=NULL; struct COGXra *COGXra=NULL; char *temparray[160]; char *giwords[5]; char *spAcc = NULL; struct slName *el, *list; char *table = tdb->table; char *pdb = hPdbFromGdb(database); struct genePred *gpList = NULL, *gp = NULL; char tableName[64]; boolean hasBin; int itemCount = 0; int arcogCount = 0; char genome[50] = ""; char clade[50] = ""; boolean hasArCOG; char treeFileName[256]; char treeTmpPsFileName[256]; char treePsFileName[256]; char treePngFileName[256]; char treePdfFileName[256]; char command[512]; char buffer[512]; char searchTerm[256]; struct blastTab *blastpHitsList; char pepTableName[64]; char extraTableName[64]; if (startsWith("annotRev", table)) { safef(pepTableName, sizeof pepTableName, "%s%s", table, pepTable); safef(extraTableName, sizeof extraTableName, "%s%s", table, extraTable); } else { safecpy(pepTableName, sizeof pepTableName, pepTable); safecpy(extraTableName, sizeof extraTableName, extraTable); } spConn = sqlConnect(UNIPROT_DB_NAME); genericHeader(tdb, item); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; if (extraTableName != NULL && hTableExists(database, extraTableName)) { sqlSafef(query, sizeof query, "select * from %s where name = '%s'", extraTableName, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { minGeneInfoStaticLoad(row, &ginfo); gi = cloneString(ginfo.gi); if (ginfo.gene != NULL && differentString(ginfo.gene,"none")) printf("<B>Gene: </B>%s<BR>\n", ginfo.gene); if (ginfo.product != NULL && differentString(ginfo.product,"none")) medlineLinkedLine("Product", ginfo.product, ginfo.product); if (ginfo.note != NULL && differentString(ginfo.note,"none")) printf("<B>Note: </B>%s<BR>\n", ginfo.note); if (ginfo.protein != NULL && differentString(ginfo.protein,"none")) printf("<B>Protein: </B>%s<BR>\n", ginfo.protein); if (ginfo.ec != NULL && differentString(ginfo.ec,"none")) { printf("<B>EC (Enzyme Commission) number:</B> " "<A HREF=\"http://us.expasy.org/enzyme/%s\" " "TARGET=_BLANK>%s</A>\n", ginfo.ec, ginfo.ec); getEcHtml(ginfo.ec); medlineLinkedTermLine("EC PubMed Search", ginfo.ec, ginfo.ec, "EC/RN Number"); printf(" <B>Brenda : </B> <A HREF=\"http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno=%s&organism=\" " "TARGET=_BLANK>%s</A><BR>\n", ginfo.ec, ginfo.ec); } } sqlFreeResult(&sr); } /* lookup swissprot acc */ spAcc = uniProtFindPrimAccFromGene(item, database); if (spAcc != NULL) { printf("<B>UniProtKB:</B> "); printf("<A HREF="); printf(uniprotFormat, spAcc); if (spAcc == NULL) { printf(" TARGET=_blank>%s</A></B><BR>\n", item); } else { printf(" TARGET=_blank>%s</A></B><BR>\n", spAcc); } } /* print table of contents */ printf("<br><hr style='width:100%%; height:2px;'><span style='font-size:larger;'>\n"); printf("<b>[<a href=\"#positions\">Positions and Sequence</a>] \n"); printf("[<a href=\"#COG\">COG</a>] \n"); printf("[<a href=\"#GO\">Gene Ontology</a>] \n"); printf("[<a href=\"#domain\">Protein Domain and Structure Infomation</a>] \n"); printf("[<a href=\"#homology\">Gene Homology</a>] \n"); printf("[<a href=\"#pathway\">Pathway</a>]</b></span> <br>\n"); printf("<hr style=\"width: 100%%; height: 2px;\"><br>\n"); /* Positions and sequence */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"positions\"></a><b>Positions and Sequence</b><br></td></tr>\n"); printf("<tr><td>\n"); hFindSplitTable(database, seqName, table, tableName, &hasBin); sqlSafefFrag(query, sizeof(query), "name = \"%s\"", item); gpList = genePredReaderLoadQuery(conn, tableName, query); for (gp = gpList; gp != NULL; gp = gp->next) { sequence = hDnaFromSeq(database, gp->chrom, gp->txStart, gp->txEnd, dnaUpper); if (sequence != NULL) printf("<B>GC content:</B> %0.2f%%<BR>\n", computeGCContent(sequence->dna, sequence->size)); } geneShowPosAndLinks(item, item, tdb, pepTableName, "htcTranslatedProtein", "htcGeneMrna", "htcGeneInGenome", "Predicted mRNA"); genePredFreeList(&gpList); printf("</td></tr></tbody></table><br>\n"); /* COG */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"COG\"></a><b>COG</b><br></td></tr>\n"); printf("<tr><td>\n"); /* cog description */ itemCount = 0; if (hTableExists(database, "COG")) { sqlSafef(query, sizeof query, "select * from COG where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { COG = COGLoad(row); if(COG!=NULL) { length=chopString(COG->COG, "," , temparray, 999); for(x=0; x<length; x++) { conn2 = hAllocConn(database); sqlSafef(query2, sizeof query2, "select * from COGXra where name = '%s'", temparray[x]); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { COGXra=COGXraLoad(row2); if(COGXra!=NULL) printf("<B>COG:</B> " "<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?%s\" target=\"_blank\" " ">%s</A> " "<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=%s\" target=\"_blank\" " ">Code %s</A> \n", COGXra->name, COGXra->name, COG->code,COG->code); printf(" %s<BR>\n", COGXra->info); itemCount++; } sqlFreeResult(&sr2); hFreeConn(&conn2); } } } sqlFreeResult(&sr); //hFreeConn(&conn2); } /* if (hTableExists(database, "arCOGs")) { struct arCOGs *infoload = NULL; struct arcogdesc *description = NULL; int rowOffset = hOffsetPastBin(database, seqName, "arCOGs"); //infoload = arCOGsLoad(row); row = NULL; sqlSafef(query, sizeof query, "select * from arCOGs where gene = '%s'", item); sr = sqlGetResult(conn, query); conn2 = hAllocConn(database); while ((row = sqlNextRow(sr)) != NULL) { infoload = arCOGsLoad(row+rowOffset); if(infoload!=NULL) { sqlSafef(query2, sizeof query2, "select * from mgCommonDb.arcogdesc where name = '%s'",infoload->name ); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { description=arcogdescLoad(row2); if(description!=NULL) { printf("<B>arCOG:</B> %s Code %s",infoload->name, description->code); printf(" %s<BR/>\n", description->description); itemCount++; } } sqlFreeResult(&sr2); hFreeConn(&conn2); } } } */ arcogCount = 0; hasArCOG = FALSE; row = NULL; sqlSafef(query, sizeof query, "show databases like 'arCogsDb'"); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { hasArCOG = TRUE; } sqlFreeResult(&sr); if (hasArCOG) { /* Get species info */ memset(genome, 0, 50); memset(clade, 0, 50); getGenomeClade(conn, database, genome, clade); sqlSafef(query, sizeof query, "select distinct a.arcog_id, a.anntation, c.class_id from arCogsDb.arcogDef a, arCogsDb.arcog b, arCogsDb.arcogFun c where a.arcog_id = b.arcog_id and a.arcog_id = c.arcog_id and db_name = '%s' and name = '%s'", database, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("<B>arCOG:</B> <A HREF=\"/arCOGsBrowser/#Tax_Tree;ArcogsId=%s\" target=\"_blank\">%s</A> <A HREF=\"/arCOGsBrowser/#MainAdvance;Genome=%s,FunId=%s,Limit=50,Index=0,Load=true\" target=\"_blank\">Code %s</A> ", row[0], row[0], genome, row[2], row[2]); printf(" %s<BR/>\n", row[1]); arcogCount++; itemCount++; } sqlFreeResult(&sr); if (arcogCount > 0) printf("<A HREF=\"/arCOGsBrowser/#MainGene;Genome=%s,Gene=%s\" target=\"_blank\">arCOG Gene Annotation</A><BR/>", genome, item); } if (itemCount == 0) printf("Not available\n"); printf("</td></tr></tbody></table><br>\n"); /* GO */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"GO\"></a><b>Gene Ontology</b><br></td></tr>\n"); printf("<tr><td>\n"); /* print go terms */ goPrint( conn, item, spAcc); printf("</td></tr></tbody></table><br>\n"); /* Protein domain and structure information */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"domain\"></a><b>Protein Domain and Structure Information</b><br></td></tr>\n"); printf("<tr><td>\n"); /* interpro domains */ list = spExtDbAcc1List(spConn, spAcc, "InterPro"); if (list != NULL) { char query[256], **row, **row2; struct sqlResult *sr, *sr2; printf("<B>InterPro Domains: </B> "); printf("<A HREF=\"http://www.ebi.ac.uk/interpro/IProteinStructures?ac=%s\" TARGET=_blank>", spAcc); printf("Graphical view of domain structure</A><BR>"); sqlSafef(query, sizeof(query), "select extAcc1,extAcc2 from extDbRef,extDb" " where extDbRef.acc = '%s'" " and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb" , spAcc); sr = sqlGetResult(spConn, query); while ((row = sqlNextRow(sr)) != NULL) { char interPro[256]; safef(interPro, 128, "%s.interProXref", pdb); if (hTableExists(database, interPro)) { sqlSafef(query, sizeof(query), "select description from %s where accession = '%s' and interProId = '%s'", interPro, spAcc, row[0]); sr2 = sqlGetResult(conn, query); if ((row2 = sqlNextRow(sr2)) != NULL) { printf("<A HREF=\"http://www.ebi.ac.uk/interpro/IEntry?ac=%s\" TARGET=_blank>", row[0]); printf("%s</A> - %s <BR>\n", row[0], row2[0]); } sqlFreeResult(&sr2); } else { printf("<A HREF=\"http://www.ebi.ac.uk/interpro/IEntry?ac=%s\" TARGET=_blank>", row[0]); printf("%s</A> - %s<BR>\n", row[0], row[1]); } } printf("<BR>\n"); slFreeList(&list); } /* pfam domains */ list = spExtDbAcc1List(spConn, spAcc, "Pfam"); if (list != NULL) { printf("<B>Pfam Domains:</B><BR>"); for (el = list; el != NULL; el = el->next) { char query[256]; char *description; sqlSafef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", el->name); description = sqlQuickString(spConn, query); if (description == NULL) { sqlSafef(query, sizeof(query), "select extDbRef.extAcc1 from extDbRef,extDb " "where extDbRef.acc = '%s' " "and extDbRef.extDb = extDb.id " "and extDb.val = '%s'" , spAcc,el->name); printf("%s\n", query); description = sqlQuickString(spConn, query); } if (description == NULL) description = cloneString("n/a"); printf("<A HREF=\"http://pfam.sanger.ac.uk/family?acc=%s\" TARGET=_blank>", el->name); printf("%s</A> - %s<BR>\n", el->name, description); freez(&description); } slFreeList(&list); printf("<BR>\n"); } list = spExtDbAcc1List(spConn, spAcc, "PDB"); if (list != NULL) { char query[256], **row; struct sqlResult *sr; int column = 0, maxColumn=4, rowCount=0; printf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>"); sqlSafef(query, sizeof(query), "select extAcc1,extAcc2 from extDbRef,extDb" " where extDbRef.acc = '%s'" " and extDb.val = 'PDB' and extDb.id = extDbRef.extDb" , spAcc); sr = sqlGetResult(spConn, query); printf("<TABLE><TR>\n"); while ((row = sqlNextRow(sr)) != NULL) { if (++column > maxColumn) { printf("</TR><TR>"); column = 1; if (rowCount == 0) { printf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn); printf("</TR><TR>"); } ++rowCount; } printf("<TD>"); printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]); if (rowCount < 1) printf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_bio_r_80.jpg\"><BR>", row[0]); printf("%s</A> - %s<BR>\n", row[0], row[1]); printf("</TD>"); } printf("</TR></TABLE>\n"); printf("<BR>\n"); slFreeList(&list); } /* Do modBase link. */ { printf("<B>ModBase Predicted Comparative 3D Structure on "); modBaseAnchor(spAcc); printf("%s", spAcc); printf("</A></B><BR>\n"); printf("<TABLE><TR>"); printf("<TD>"); modBaseAnchor(spAcc); - printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s\"></A></TD>", spAcc); + printf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", spAcc); printf("<TD>"); modBaseAnchor(spAcc); - printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", spAcc); + printf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", spAcc); printf("<TD>"); modBaseAnchor(spAcc); - printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", spAcc); + printf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", spAcc); printf("</TR><TR>\n"); printf("<TD ALIGN=CENTER>Front</TD>"); printf("<TD ALIGN=CENTER>Top</TD>"); printf("<TD ALIGN=CENTER>Side</TD>"); printf("</TR></TABLE>\n"); printf("<I>The pictures above may be empty if there is no " "ModBase structure for the protein. The ModBase structure " "frequently covers just a fragment of the protein. You may " "be asked to log onto ModBase the first time you click on the " "pictures. It is simplest after logging in to just click on " "the picture again to get to the specific info on that model.</I><p>"); } printf("</td></tr></tbody></table><br>\n"); /* Gene Homology */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"homology\"></a><b>Gene Homology</b><br></td></tr>\n"); printf("<tr><td>\n"); /* ncbi blast hits */ hits = chopString(gi,":",giwords,sizeof(giwords)); if (hits > 0) { printf("<B>NCBI Blast Hits:</B> " "<A HREF=\"http://www.ncbi.nlm.nih.gov/sutils/blink.cgi?pid=%s\" " "TARGET=_BLANK>%s</A><BR>\n", (hits == 2) ? giwords[1] : giwords[0], (hits == 2) ? giwords[1] : giwords[0]); } /* Gene tree */ safef(treeFileName, sizeof(treeFileName), "../trash/geneTree/geneTree_%s.txt", item); if (getGeneTree(conn, item, treeFileName)) { safef(treeTmpPsFileName, sizeof(treeTmpPsFileName), "../trash/geneTree/tmp_geneTree_%s.ps", item); safef(treePsFileName, sizeof(treePsFileName), "../trash/geneTree/geneTree_%s.ps", item); safef(treePngFileName, sizeof(treePngFileName), "../trash/geneTree/geneTree_%s.png", item); safef(treePdfFileName, sizeof(treePdfFileName), "../trash/geneTree/geneTree_%s.pdf", item); safef(searchTerm, sizeof(searchTerm), ".%s) show\n", item); if (!fileExists(treePsFileName)) { safef(command, sizeof(command), "../bin/draw_tree -b %s | grep -v translate | sed '5 i 10 530 translate' | sed '6 i 0.33 0.33 scale' | sed 's/findfont 12/findfont 24/' > %s", treeFileName, treeTmpPsFileName); mustSystem(command); FILE *fi = mustOpen(treeTmpPsFileName, "r"); FILE *fo = mustOpen(treePsFileName, "w"); if ((fi != NULL) && (fo != NULL)) { mustGetLine(fi, buffer, 512); while (!sameWord(buffer, "")) { if (endsWith(buffer, searchTerm)) { fprintf(fo, "255 0 0 setrgbcolor\n"); fprintf(fo, "%s", buffer); fprintf(fo, "0 0 0 setrgbcolor\n"); } else fprintf(fo, "%s", buffer); mustGetLine(fi, buffer, 512); } fclose(fo); fclose(fi); } safef(command, sizeof(command), "rm -f %s", treeTmpPsFileName); mustSystem(command); } if (!fileExists(treePngFileName)) { safef(command, sizeof(command), "pstoimg -scale 0.4 -aaliastext -type png -density 300 -out %s %s", treePngFileName, treePsFileName); mustSystem(command); } if (!fileExists(treePdfFileName)) { safef(command, sizeof(command), "ps2pdf %s %s", treePsFileName, treePdfFileName); mustSystem(command); } printf("<BR><B>Phylogenetic tree with homologous genes:</B> View as \n"); printf("<A HREF=\"%s\" TARGET=_BLANK>Postscript</A> \n", treePsFileName); printf("<A HREF=\"%s\" TARGET=_BLANK>PNG</A> \n", treePngFileName); printf("<A HREF=\"%s\" TARGET=_BLANK>PDF</A> \n", treePdfFileName); printf("<A HREF=\"%s\" TARGET=_BLANK>Text</A> <BR>\n", treeFileName); printf("<BR>The 20 highest scoring homologous genes of this protein were retrieved by BLASTP from the genomes available in the UCSC microbial genome browser. "); printf("The alignments of the protein sequences, made by <A HREF=\"http://www.drive5.com/muscle/\" TARGET=_BLANK>MUSCLE</A>, "); printf("were used to construct the phylogenetic tree. This maximum likelihood unrooted tree was computed by using "); printf("<A HREF=\"http://www.atgc-montpellier.fr/phyml/\" TARGET=_BLANK>PHYML</A> with the Jones Taylor Thornton model of sequence evolution, "); printf("by including a Gamma-correction (eight categories of evolutionary rates, "); printf("an estimated alpha-parameter and an estimated proportion of invariant sites).<BR>"); } /* Self Homologs */ if (selfBlastpHitCount(conn, item) > 0) { blastpHitsList = loadSelfBlastpHits(conn, item, 0); printSelfHomologs(conn, blastpHitsList); } printf("</td></tr></tbody></table><br>\n"); /* Pathway */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"pathway\"></a><b>Pathway</b><br></td></tr>\n"); printf("<tr><td>\n"); /* kegg pathway links */ if (keggCount(conn, item) > 0) { keggLink(conn, item, table, "<B>Kegg Pathway: </b><BR>"); } else printf("Not available\n"); printf("</td></tr></tbody></table><br>\n"); /* Do SAM-T02 sub-section */ //doSamT02(spAcc, database); printTrackHtml(tdb); hFreeConn(&conn); } /*Code to display Sargasso Sea Information*/ void doSargassoSea(struct trackDb *tdb, char *trnaName) { struct bed *cb=NULL; struct sargassoSeaXra *cbs=NULL, *cbs2, *list=NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; char *dupe, *words[16]; char **row; char tempstring[255]=""; int z, dashes, wordCount; int start = cartInt(cart, "o"), num = 0; float sequenceLength, dashlength=60; genericHeader(tdb,trnaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, trnaName, start, num); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, trnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) cb=bedLoadN(row+1, 6); sequenceLength=(cb->chromEnd - cb->chromStart); if(sequenceLength<0){ sequenceLength=sequenceLength*-1;} sequenceLength=sequenceLength/3; dashlength=sequenceLength/60; /*Query the database for the extrainfo file for sargassoSea*/ conn=hAllocConn(database);/*sqlConnect(dupe);*/ sqlSafef(tempstring, sizeof(tempstring),"select * from sargassoSeaXra where qname = '%s'", trnaName); sr = sqlGetResult(conn, tempstring); /*Load the required data from the database*/ while ((row = sqlNextRow(sr)) != NULL) { cbs=sargassoSeaXraLoad(row); slAddHead(&list, cbs); } slReverse(&list); /*Print out table with Blast information*/ printf(" </tbody>\n</table>\n<br><br>"); printf("<table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"text-align: left; width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Nucleotides \naligned begin</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Nucelotides \naligned end</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>NCBI Link</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Evalue</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Percent Identity</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Alignment Length</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Gap openings</b>"); printf("</td>\n </tr>\n <tr>"); for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { printf("\n \n <td style=\"vertical-align: top;\">"); printf("<a name=\"%i-desc\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-align\">%s</a>",cbs2->GI,cbs2->species); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->thisseqstart); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->thisseqend); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=%i\">NCBI Link</a>",cbs2->GI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->evalue); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%.2f",cbs2->PI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->length); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->gap); printf("<br></td>\n </tr>\n"); } /* printf(" <br><br></tbody>\n</table> \n"); */ /*Print out the table for the alignments*/ printf("<table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>Alignment</b>"); printf("</td>\n </tr>\n <tr>"); printf(" <td style=\"vertical-align: top;\">%s where each plus(+) is approx. %.1f amino acids", trnaName, dashlength); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); for(z=0; z<60; z++) { printf("+"); } printf("</code>"); printf("</td>\n </tr>\n <tr>"); for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { printf("\n </td>\n <td style=\"vertical-align: top;\">"); dashes=cbs2->queryseqstart-cbs2->queryseqend; if(dashes<0) dashes=dashes*-1; printf("<a name=\"%i-align\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-desc\">%s</a>, %s",cbs2->GI, cbs2->species,cbs2->qName); printf("\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); dashes=dashes/dashlength; if(cbs2->queryseqstart>cbs2->queryseqend) for(z=0; z<((cbs2->queryseqend)/dashlength); z++) { printf(" "); } else for(z=0; z<((cbs2->queryseqstart)/dashlength); z++) { printf(" "); } if(dashes<1) printf("+"); for(z=0; z<dashes; z++) printf("+"); printf("</code>"); printf("</td>\n </tr>\n"); } /*Free the data*/ hFreeConn(&conn); sargassoSeaXraFree(&cbs); printTrackHtml(tdb); } /*Function to print out full code name from code letter*/ void printCode(char code) { switch(code) { case 'a': printf("Aerobe"); break; case 'b': printf("Bacteria"); break; case 'c': printf("Crenarchaea"); break; case 'd': printf("Acidophile"); break; case 'e': printf("Euryarchaea"); break; case 'g': printf("Within Genus"); break; case 'h': printf("Hyperthermophile"); break; case 'm': printf("Methanogen"); break; case 'n': printf("Anaerobe"); break; case 'o': printf("Nanoarchaea"); break; case 't': printf("Thermophile"); break; case 'u': printf("Eukarya"); break; case 'v': printf("Viral"); break; case 'k': printf("Alkaliphile"); break; case 'l': printf("Halophile"); break; case 'r': printf("Facultative Aerobe"); break; default: break; } } void doTrnaGenes(struct trackDb *tdb, char *trnaName) { struct tRNAs *trna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; char* chrom = cartString(cart, "c"); genericHeader(tdb,trnaName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and name = '%s'", tdb->table, chrom, trnaName); sr = sqlGetResult(conn, query); printf("<TABLE>\n"); while ((row = sqlNextRow(sr)) != NULL) { printf("<TR>\n"); printf("<TD valign=top>\n"); 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<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 tRNA alignments</A><BR>\n", trna->trnaUrl); } if (trna->next != NULL) printf("<hr>\n"); printf("</TD>\n"); printf("<TD>\n"); if (startsWith(trna->chrom, trna->name)) printf("<img align=right src=\"../RNA-img/%s/%s-%s.gif\" alt='tRNA secondary structure for %s'>\n", database,database,trna->name,trna->name); else printf("<img align=right src=\"../RNA-img/%s/%s-%s-%s.gif\" alt='tRNA secondary structure for %s'>\n", database,database,trna->chrom,trna->name,trna->name); printf("</TD>"); printf("</TR>"); } printf("</TABLE>"); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); tRNAsFree(&trna); } void doSnornaGenes(struct trackDb *tdb, char *snornaName) { struct snoRNAs *snorna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; genericHeader(tdb,snornaName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, snornaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { snorna = snoRNAsLoad(row+rowOffset); printf("<B>sRNA name: </B> %s<BR>\n",snorna->name); printf("<B>Snoscan score: </B> %.2f<BR>\n",snorna->snoScore); printf("<B>HMM snoRNA score: </B> %.2f<BR>\n",snorna->hmmScore); printf("<B>Predicted targets: </B> %s<BR>\n",snorna->targetList); printf("<B>Predicted guide interactions:</B><pre>%s</pre>\n",snorna->guideStr); printf("<B>Possible sRNA homolog(s): </B> %s<BR>\n",snorna->orthologs); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",snorna->chromEnd-snorna->chromStart); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, snorna->chrom, snorna->chromStart+1, snorna->chromEnd); printf("%s:%d-%d</A><BR>\n", snorna->chrom, snorna->chromStart+1, snorna->chromEnd); printf("<B>Strand:</B> %s<BR><BR>\n", snorna->strand); printf("<B>Snoscan program output: </B><BR><pre> %s</pre><BR>\n",snorna->snoscanOutput); if (snorna->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); snoRNAsFree(&snorna); } void doGbRnaGenes(struct trackDb *tdb, char *gbRnaName) { struct gbRNAs *gbRna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; genericHeader(tdb,gbRnaName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, gbRnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { gbRna = gbRNAsLoad(row+rowOffset); printf("<B>Genbank ncRNA name: </B> %s<BR>\n",gbRna->name); printf("<B>Product Description/Note: </B> %s<BR>\n",gbRna->product); printf ("<B>Intron(s): </B> %s<BR>\n",gbRna->intron); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",gbRna->chromEnd-gbRna->chromStart); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, gbRna->chrom, gbRna->chromStart+1, gbRna->chromEnd); printf("%s:%d-%d</A><BR>\n", gbRna->chrom, gbRna->chromStart+1, gbRna->chromEnd); printf("<B>Strand:</B> %s<BR>\n", gbRna->strand); if (gbRna->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); gbRNAsFree(&gbRna); } void doEasyGenes(struct trackDb *tdb, char *egName) { struct easyGene *egList = NULL, *eg; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; genericHeader(tdb,egName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, egName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) slAddTail(&egList,easyGeneLoad(row+rowOffset)); slReverse(&egList); sqlFreeResult(&sr); hFreeConn(&conn); for (eg = egList; eg != NULL; eg = eg->next) { if (eg->genbank[0] == 'Y') printf("<span style='color:#FF0000;'>\n"); else printf("<span style='color:#000000;'>\n"); printf("<B>Item:</B> %s<BR>\n",eg->name); printf("<B>Feature identifier:</B> %s<BR>\n",eg->feat); printf("<B>Start codon:</B> %s<BR>\n",eg->startCodon); printf("<B>EasyGene descriptor:</B> %s<BR>\n",eg->descriptor); if (eg->R >= 0.001) printf("<B>R value:</B> %.3f<BR>\n",eg->R); else printf("<B>R value:</B> %.2e<BR>\n",eg->R); printf("<B>Log-odds :</B> %.1f<BR>\n",eg->logOdds); printf("<B>Frame:</B> %d<BR>\n",eg->frame); printf("<B>Swiss-Prot match:</B> %s<BR>\n",eg->swissProt); printf("<B>ORF identifier:</B> %s<BR>\n",eg->orf); printPos(eg->chrom, eg->chromStart, eg->chromEnd, eg->strand, TRUE, eg->name); printf("</span>\n"); if (eg->next != NULL) printf("<hr>\n"); } printTrackHtml(tdb); easyGeneFreeList(&egList); } void doCodeBlast(struct trackDb *tdb, char *trnaName) { struct pepPred *pp=NULL; struct codeBlast *cb=NULL; struct codeBlastScore *cbs=NULL, *cbs2, *list=NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; char *dupe, *words[16]; char **row; char tempstring[255]=""; int flag, z, dashes, wordCount, currentGI=0; int start = cartInt(cart, "o"), num = 0; float sequenceLength, dashlength=60; genericHeader(tdb,trnaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, trnaName, start, num); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, trnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cb=codeBlastLoad(row); } sequenceLength=(cb->chromEnd - cb->chromStart); if(sequenceLength<0){ sequenceLength=sequenceLength*-1;} sequenceLength=sequenceLength/3; dashlength=sequenceLength/60; conn=hAllocConn(database);/*sqlConnect(dupe);*/ sqlSafef(query, sizeof query, "select * from gbProtCodePep where name = '%s'", trnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { pp=pepPredLoad(row); } /*Query the database for the extrainfo file for codeBlast*/ conn=hAllocConn(database);/*sqlConnect(dupe);*/ sqlSafef(tempstring, sizeof(tempstring), "select * from codeBlastScore where qname = '%s'", trnaName); sr = sqlGetResult(conn, tempstring); /*Load the required data from the database*/ while ((row = sqlNextRow(sr)) != NULL) { cbs=codeBlastScoreLoad(row); slAddHead(&list, cbs); } if (pp!=NULL) printf( "<br><a\nhref=\"http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=Semiauto&CDD_SEARCH=on&CLIENT=web&DATABASE=nr&DESCRIPTIONS=500&ENTREZ_QUERY=All+organisms&EXPECT=10&FILTER=L&FORMAT_BLOCK_ON_RESPAGE=None&FORMAT_ENTREZ_QUERY=All+organisms&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GAPCOSTS=11+1&GET_SEQUENCE=on&I_THRESH=0.005&LAYOUT=TwoWindows&MASK_CHAR=0&MASK_COLOR=0&MATRIX_NAME=BLOSUM62&NCBI_GI=on&NEW_FORMATTER=on&PAGE=Proteins&PROGRAM=blastp&QUERY=%s&SERVICE=plain&SET_DEFAULTS=Yes&SET_DEFAULTS.x=25&SET_DEFAULTS.y=11&SHOW_LINKOUT=on&SHOW_OVERVIEW=on&WORD_SIZE=3&END_OF_HTTPGET=Yes\">Query NCBI Blast",pp->seq); /*Print out table with Blast information*/ printf(" </tbody>\n</table>\n<br><br><table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"text-align: left; width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Phylogenetic/Functional Category</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Gene Name</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Product</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>NCBI Entry</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Evalue</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Percent Identity</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Alignment Length(AA)</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Gap openings</b>"); printf("</td>\n </tr>\n <tr>"); flag=0; for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { if(sameString(trnaName, cbs2->qName)) { if(flag==0) { currentGI=cbs2->GI; printf("\n \n <td style=\"vertical-align: top;\">"); printf("<a name=\"%i-desc\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-align\">%s</a>",cbs2->GI,cbs2->species); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); flag=1; } if((cbs2->next!=NULL) && (currentGI== cbs2->GI) && (currentGI== cbs2->next->GI) ) { printCode(cbs2->code[0]); printf(", "); } else { printCode(cbs2->code[0]); /*See which database to link to*/ if((sameString(cbs2->species, "Pyrococcus furiosus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrFur2&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Pyrococcus abyssi"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrAby1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Pyrococcus horikoshii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrHor1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermococcus kodakaraensis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therKoda1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Sulfolobus solfataricus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=sulSol1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Sulfolobus tokodaii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=sulfToko1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Sulfolobus acidocaldarius"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=sulfAcid1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Pyrobaculum aerophilum"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrAer1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Nanoarchaeum equitans"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=nanEqu1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosarcina acetivorans"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=metAce1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosarcina barkeri"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methBark1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosarcina mazei"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methMaze1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanothermobacter thermautotrophicus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methTher1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanococcoides burtonii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methBurt1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanopyrus kandleri"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methKand1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Haloarcula marismortui"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=halMar1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Halobacterium sp."))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=haloHalo1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Aeropyrum pernix"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=aerPer1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Archaeoglobus fulgidus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=archFulg1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermoplasma acidophilum"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therAcid1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermoplasma volcanium"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therVolc1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanocaldococcus jannaschii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methJann1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanococcus maripaludis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=metMar1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosphaera stadtmanae"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methStad1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanospirillum hungatei"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methHung1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Aquifex aeolicus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=aquiAeol1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermotoga maritima"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therMari1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Escherichia coli K12"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=eschColi_K12_1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Bacillus subtilis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=baciSubt1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Shewanella oneidensis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=shewOnei1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else{ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->name); } printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->product); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=%i\">NCBI Link</a>",cbs2->GI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->evalue); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%.2f",cbs2->PI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->length); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->gap); printf("<br></td>\n </tr>\n"); flag=0; } } } /*Print out the table for the alignments*/ printf("</td></td></td><br>\n<table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>Alignment</b>"); printf("</td>\n </tr>\n <tr>"); printf(" <td style=\"vertical-align: top;\">%s where each plus(+) is approx. %f amino acids", trnaName, dashlength); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); for(z=0; z<60; z++) { printf("+"); } printf("</code>"); printf("</td>\n </tr>\n <tr>"); flag=0; for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { if(sameString(trnaName, cbs2->qName)) { if(flag==0) { currentGI=cbs2->GI; printf("\n </td>\n <td style=\"vertical-align: top;\">"); flag=1; } if((cbs2->next!=NULL) && (currentGI== cbs2->GI) && (currentGI== cbs2->next->GI) ) { } else { dashes=cbs2->seqend-cbs2->seqstart; if(cbs2->length<dashes/2){dashes=dashes/3;} if(dashes<0) dashes=dashes*-1; printf("<a name=\"%i-align\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-desc\">%s</a>, %s",cbs2->GI, cbs2->species, cbs2->name); printf("\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); dashes=dashes/dashlength; if(cbs2->seqstart>cbs2->seqend) for(z=0; z<((cbs2->seqend)/dashlength); z++) { printf(" "); } else for(z=0; z<((cbs2->seqstart)/dashlength); z++) { printf(" "); } if(dashes<1) printf("+"); for(z=0; z<dashes; z++) printf("+"); printf("</code>"); printf("</td>\n </tr>\n"); flag=0; } } } printf(" <br><br></tbody>\n</table> \n"); /*\printf(" </tbody>\n</table> \n"); */ /*Free the data*/ hFreeConn(&conn); codeBlastScoreFree(&cbs); codeBlastFree(&cb); printTrackHtml(tdb); } void llDoCodingGenes(struct trackDb *tdb, char *item, char *pepTable, char *extraTable) /* Handle click on gene track. */ { struct minGeneInfo ginfo; char query[256]; char query2[256]; struct sqlResult *sr, *sr2; char **row, **row2; char *words[16], *dupe = cloneString(tdb->type); int wordCount, x, length; int start = cartInt(cart, "o"), num = 0; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2; struct COG *COG=NULL; struct COGXra *COGXra=NULL; char *temparray[160]; genericHeader(tdb, item); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, item, start, num); if (pepTable != NULL && hTableExists(database, pepTable)) { char *pepNameCol = sameString(pepTable, "gbSeq") ? "acc" : "name"; conn = hAllocConn(database); /* simple query to see if pepName has a record in pepTable: */ sqlSafef(query, sizeof(query), "select 0 from %s where %s = '%s'", pepTable, pepNameCol, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { hgcAnchorSomewhere("htcTranslatedProtein", item, pepTable, seqName); printf("Predicted Protein</A> <BR>\n"); } sqlFreeResult(&sr); } if (extraTable != NULL && hTableExists(database, extraTable)) { conn = hAllocConn(database); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", extraTable, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { minGeneInfoStaticLoad(row, &ginfo); printf("<B>Product: </B>%s<BR>\n", ginfo.product); printf("<B>Note: </B>%s<BR>\n", ginfo.note); } sqlFreeResult(&sr); } if (hTableExists(database, "COG")) { conn = hAllocConn(database); sqlSafef(query, sizeof query, "select * from COG where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { COG = COGLoad(row); if(COG!=NULL) { length=chopString(COG->COG, "," , temparray, 999); for(x=0; x<length; x++) { conn2 = hAllocConn(database); sqlSafef(query2, sizeof query2, "select * from COGXra where name = '%s'", temparray[x]); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { COGXra=COGXraLoad(row2); if(COGXra!=NULL) printf("<B>COG: </B>%s <B>INFO: </B>%s<BR>\n", COGXra->name, COGXra->info); } sqlFreeResult(&sr2); hFreeConn(&conn2); } } } } printTrackHtml(tdb); hFreeConn(&conn); } /*void doTigrOperons(struct trackDb *tdb, char *opName)*/ /* track handler for the TIGR operon predictions */ /*{ struct tigrOperon *op; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int start = cartInt(cart, "o"), num = 0; genericHeader(tdb,opName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, opName, start, num); sqlSafef(query, sizeof query, "select * from %sInfo where name = '%s'", tdb->table, opName); sr = sqlGetResult(conn, query);*/ /* Make the operon table like on the TIGR web page. */ /*if ((row = sqlNextRow(sr)) != NULL) { int i,j; char *infos[30]; op = tigrOperonLoad(row); chopCommas(op->info,infos); printf("<P>\n<TABLE BORDER=1 ALIGN=\"CENTER\">\n"); for (i = 0; i <= op->size; i++) { printf(" <TR ALIGN=\"CENTER\">"); for (j = 0; j <= op->size; j++) { printf("<TD>"); if ((i == 0 || j == 0) && !(i == 0 && j == 0)) (i > j) ? printf("%s",op->genes[i-1]) : printf("%s",op->genes[j-1]); else if (i + j > 0) { char *data = infos[((i-1)*op->size)+(j-1)]; if (!sameString(data,"---")) { char *n, *conf; n = chopPrefixAt(data,'|'); conf = data; printf("confidence = %.2f, n = %d",atof(conf),atoi(n)); } else printf("%s",data); } printf("</TD>"); } printf("</TR>\n"); } printf("</TABLE>\n</P>\n"); } printTrackHtml(tdb);*/ /* clean up */ /*sqlFreeResult(&sr); hFreeConn(&conn); tigrOperonFree(&op); } */ void doTigrCmrGene(struct trackDb *tdb, char *tigrName) /* Handle the TIRG CMR gene track. */ { struct tigrCmrGene *tigr; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; genericHeader(tdb,tigrName); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, tigrName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigr = tigrCmrGeneLoad(row); if (tigr != NULL) { printf("<B>TIGR locus name: </B> %s<BR>\n",tigrName); printf("<B>TIGR gene description: </B> %s<BR>\n",tigr->tigrCommon); printf("<B>Alternate TIGR gene name: </B> "); if (strlen(tigr->tigrGene) >0) { printf("%s<BR>\n",tigr->tigrGene); } else { printf("None<BR>"); } printf("<B>Genbank locus name: </B> %s<BR>\n",tigr->primLocus); printf("<B>Protein length: </B> %d aa<BR>\n",tigr->tigrPepLength); if (strlen(tigr->tigrECN)>0) { printf("<B>Enzyme comission number: </B> %s<BR>\n",tigr->tigrECN); } printf("<B>Main role: </B> %s<BR>\n",tigr->tigrMainRole); printf("<B>Subrole: </B> %s<BR>\n",tigr->tigrSubRole); if (tigr->tigrMw > 0) { printf("<B>Molecular weight: </B> %.2f Da<BR>\n",tigr->tigrMw); } if (tigr->tigrPi > 0) { printf("<B>Isoelectric point: </B> %.2f<BR>\n",tigr->tigrPi); } printf("<B>GC content: </B> %.2f %%<BR>\n",tigr->tigrGc); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, tigr->chrom, tigr->chromStart, tigr->chromEnd); printf("%s:%d-%d</A><BR>\n", tigr->chrom, tigr->chromStart, tigr->chromEnd); printf("<B>Strand:</B> %s<BR>\n", tigr->strand); printf("<B>Genomic size: </B> %d nt<BR>\n",tigr->tigrLength); if (tigr->next != NULL) printf("<hr>\n"); } } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); tigrCmrGeneFree(&tigr); } void doJgiGene(struct trackDb *tdb, char *jgiName) /* Handle the JGI gene track. */ { struct jgiGene *jgi; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; genericHeader(tdb,jgiName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, jgiName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { jgi = jgiGeneLoad(row+rowOffset); printf("<B>JGI locus name: </B> %s<BR>\n",jgiName); printf("<B>JGI gene symbol: </B> %s<BR>\n",jgi->jgiSymbol); printf("<B>JGI gene description: </B> %s<BR>\n",jgi->jgiDescription); printf("<B>JGI gene id:</B> " "<A HREF=\"http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=%s\" TARGET=_blank>", jgi->jgiGeneId); printf("%s</A><BR>\n", jgi->jgiGeneId); printf("<B>GC content: </B> %.0f %%<BR>\n",jgi->jgiGc); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, jgi->chrom, jgi->chromStart + 1, jgi->chromEnd); printf("%s:%d-%d</A><BR>\n", jgi->chrom, jgi->chromStart + 1, jgi->chromEnd); printf("<B>Strand:</B> %s<BR>\n", jgi->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (jgi->chromEnd - jgi->chromStart)); if (jgi->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); jgiGeneFree(&jgi); } void doPfamHit(struct trackDb *tdb, char *hitName) /* Handle the Pfam hits track. */ { struct lowelabPfamHits *pfamHit; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *spConn = NULL; struct sqlResult *sr; char **row; int rowOffset; char *description; int start = cartInt(cart, "o"); spConn = sqlConnect(UNIPROT_DB_NAME); genericHeader(tdb,hitName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, hitName,seqName,start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { pfamHit = lowelabPfamHitsLoad(row+rowOffset); sqlSafef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", pfamHit->pfamAC); if (!sqlTableExists(spConn,"proteome.pfamDesc")) { sqlSafef(query, sizeof(query), "select extDbRef.extAcc1 from extDbRef,extDb " "where extDbRef.acc = '%s' " "and extDbRef.extDb = extDb.id " "and extDb.val = '%s'" , pfamHit->pfamAC,pfamHit->pfamID); } description = sqlQuickString(spConn, query); if (description == NULL) description = cloneString("n/a"); printf("<A HREF=\"http://pfam.sanger.ac.uk/family?acc=%s\" TARGET=_blank>", pfamHit->pfamAC ); printf("%s</A> - %s<BR><BR>\n", pfamHit->pfamAC, description); freez(&description); if (pfamHit->ident > 0) printf("<B>Domain assignment based on %d%% identity BlastP hit to Pfam-A SwissProt Sequence:</B><BR>\n" "<A HREF=\"http://www.expasy.org/uniprot/%s\">%s</A> (%s, %d%% full-length alignment) " "<BR><A HREF=\"http://pfam.sanger.ac.uk/protein/%s\">[Pfam Domain Structure]</A><BR>\n", pfamHit->ident,pfamHit->swissAC,pfamHit->swissAC,pfamHit->protCoord,pfamHit->percLen,pfamHit->swissAC); else { printf("<B>Gene:</B> %s<BR><BR>\n", pfamHit->pfamID); printf("<B>Domain assignment based on Pfam model search using HMMER 3.0</B><BR>\n" "E-value: %s<BR>(%s, %d%% full-length)<BR>\n", pfamHit->swissAC,pfamHit->protCoord,pfamHit->percLen); } printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, pfamHit->chrom, pfamHit->chromStart + 1, pfamHit->chromEnd); printf("%s:%d-%d</A><BR>\n", pfamHit->chrom, pfamHit->chromStart + 1, pfamHit->chromEnd); printf("<B>Strand:</B> %s<BR>\n", pfamHit->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (pfamHit->chromEnd - pfamHit->chromStart)); if (pfamHit->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); lowelabPfamHitsFree(&pfamHit); } void doTigrOperons(struct trackDb *tdb, char *tigrOperonName) /* Handle the TIGR operons track. */ { struct bed *tigrOperon; struct lowelabTIGROperonScore *tigrOperonScore; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; genericHeader(tdb, tigrOperonName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, tigrOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigrOperon = bedLoadN(row+rowOffset, bedSize); printf("<B>Operon name: </B> %s<BR>\n",tigrOperonName); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("%s:%d-%d</A><BR>\n", tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("<B>Strand:</B> %s<BR>\n", tigrOperon->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (tigrOperon->chromEnd - tigrOperon->chromStart)); if (tigrOperon->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>OperonDB predicted gene pairs</B><br>\n"); /* Print table */ printf("<table style=\"width: 50%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 " "cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"25%%\"><b>Gene 1</b></td>\n"); printf("<td width=\"25%%\"><b>Gene 2</b></td>\n"); printf("<td width=\"25%%\"><b>Confidence</b></td>\n"); printf("<td width=\"25%%\"><b>Number of Conserved Genomes</b></td>\n"); printf("</tr>\n"); sqlSafef(query, sizeof query, "select * from lowelabTIGROperonScore where name = '%s'", tigrOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigrOperonScore = lowelabTIGROperonScoreLoad(row); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td>%s</td>\n", tigrOperonScore->gene1); printf("<td>%s</td>\n", tigrOperonScore->gene2); printf("<td style=\"text-align: right;\">%d</td>\n", tigrOperonScore->confidence); printf("<td style=\"text-align: right;\"><A HREF=\"%s\">%d</A></td>\n", tigrOperonScore->ortholog_link, tigrOperonScore->ortholog); printf("</tr>\n"); tigrOperonScore = tigrOperonScore->next; } sqlFreeResult(&sr); /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); printf("<br>Note:\n"); printf("<br>Confidence - an estimation of the lower boundary of the probability that the two corresponding genes are located in the same operon\n"); printf("<br>Number of Conserved Genomes - number of other genomes that have the same pair of genes located in the same directon (a set of consecutive genes on the same DNA strand)\n"); bedFree(&tigrOperon); lowelabTIGROperonScoreFree(&tigrOperonScore); hFreeConn(&conn); printTrackHtml(tdb); } void doArkinOperons(struct trackDb *tdb, char *arkinOperonName) /* Handle the Arkin operons track. */ { struct bed *arkinOperon; struct lowelabArkinOperonScore *arkinOperonScore; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; genericHeader(tdb, arkinOperonName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, arkinOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { arkinOperon = bedLoadN(row+rowOffset, bedSize); printf("<B>Arkin operon name: </B> %s<BR>\n",arkinOperonName); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("%s:%d-%d</A><BR>\n", arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("<B>Strand:</B> %s<BR>\n", arkinOperon->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (arkinOperon->chromEnd - arkinOperon->chromStart)); if (arkinOperon->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>Arkin operon predicted gene pairs</B><br>\n"); /* Print table */ printf("<table style=\"width: 50%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 " "cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"25%%\"><b>Gene 1</b></td>\n"); printf("<td width=\"25%%\"><b>Gene 2</b></td>\n"); printf("<td width=\"25%%\"><b>Probability of the Same Operon</b></td>\n"); printf("<td width=\"25%%\"><b>Gene neighbor score</b></td>\n"); printf("</tr>\n"); sqlSafef(query, sizeof query, "select * from lowelabArkinOperonScore where name = '%s'", arkinOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { arkinOperonScore = lowelabArkinOperonScoreLoad(row); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td>%s</td>\n", arkinOperonScore->gene1); printf("<td>%s</td>\n", arkinOperonScore->gene2); printf("<td style=\"text-align: right;\">%0.3f</td>\n", arkinOperonScore->prob); printf("<td style=\"text-align: right;\">%0.3f</td>\n", arkinOperonScore->gnMinus); printf("</tr>\n"); arkinOperonScore = arkinOperonScore->next; } sqlFreeResult(&sr); /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); printf("<br>Note:\n"); printf("<br>Probability of the Same Operon - Estimated probability that the pair is in the same operon. Values near 1 or 0 are confident predictions of being in the same operon or not, while values near 0.5 are low-confidence predictions.\n"); printf("<br>Gene neighbor score - An indicator of conservation (gene neighbor score, surprisal subtracted). Positive scores indicate conservation, and scores above 5 are generally strongly indicative of operons\n"); bedFree(&arkinOperon); lowelabArkinOperonScoreFree(&arkinOperonScore); hFreeConn(&conn); printTrackHtml(tdb); } struct bed * getBlastpTrackRecord(struct sqlConnection *conn, struct trackDb *tdb, char *targetName) /* Get blastp track record clicked by user*/ { struct bed *blastpTrack = NULL; char *dupe, *words[16]; int wordCount; int bedSize = 0; char query[512]; struct sqlResult *sr; char **row; int rowOffset; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *chrom = cartString(cart, "c"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select distinct * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = %d", tdb->table, targetName, chrom, start, end); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) blastpTrack = bedLoadN(row+rowOffset, bedSize); freez(&dupe); sqlFreeResult(&sr); return blastpTrack; } void printQueryGeneInfo(struct sqlConnection *conn, struct bed *blastpTrack, char *queryName, unsigned int *querySeqLength, char *queryTable) /* Get and print blastp query gene info */ { char query[512]; struct sqlResult *srRefSeq; char **row; int geneCount; char **buffer = NULL; char *targetGeneName[2]; struct minGeneInfo* ginfo; char blastpHits[] = "blastpHits"; unsigned int queryStart = 0; unsigned int queryEnd = 0; parseDelimitedString(blastpTrack->name, ':', targetGeneName, 2); if (hTableExists(database, queryTable) && hTableExists(database, blastpHits)) { /* Get query gene from refSeq */ sqlSafef(query, sizeof query, "select count(*) from %s where chrom = '%s' and strand = '%s' and cdsStart <= %u and cdsEnd >= %u", queryTable, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd); srRefSeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srRefSeq)) != NULL) { geneCount = atoi(row[0]); sqlFreeResult(&srRefSeq); if (geneCount == 1) { sqlSafef(query, sizeof query, "select name, cdsStart, cdsEnd from %s where chrom = '%s' and strand = '%s' and cdsStart <= %u and cdsEnd >= %u", queryTable, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd); srRefSeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srRefSeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srRefSeq); } else { /* Check blastpHits if more than 1 query gene is found within the region */ sqlSafef(query, sizeof query, "select a.name, a.cdsStart, a.cdsEnd from %s a, %s b where a.chrom = '%s' and a.strand = '%s' and a.cdsStart <= %u and a.cdsEnd >= %u and a.name = b.query and b.target like '%%%s'", queryTable, blastpHits, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd, targetGeneName[0]); srRefSeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srRefSeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srRefSeq); } if ((queryStart == 0) && (queryEnd == 0)) printf("Query gene not found for %s at %s:%u-%u\n", blastpTrack->name, blastpTrack->chrom, blastpTrack->chromStart, blastpTrack->chromEnd); else { *querySeqLength = queryEnd - queryStart; /* Print query gene info */ printf("<B>Gene: </B>%s<BR>\n", queryName); ginfo = getGbProtCodeInfo(conn, database, queryName); if (ginfo != NULL) { if (ginfo->product != NULL && differentString(ginfo->product,"none")) medlineLinkedLine("Product", ginfo->product, ginfo->product); } printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, blastpTrack->chrom, queryStart + 1, queryEnd); printf("%s:%d-%d</A><BR>\n", blastpTrack->chrom, queryStart + 1, queryEnd); printf("<B>Strand:</B> %s<BR>\n", blastpTrack->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (queryEnd - queryStart)); } } else printf("<BR>Query gene not found for %s at %s:%u-%u<BR>\n", blastpTrack->name, blastpTrack->chrom, blastpTrack->chromStart, blastpTrack->chromEnd); } sqlFreeResult(&srRefSeq); free(targetGeneName[0]); free(targetGeneName[1]); } struct slName* getAllClades(struct sqlConnection *conn) /* Get all available clades in database */ { char query[512]; struct sqlResult *srDb; char **rowDb; struct slName *list = NULL; char clade[50]; sqlSafef(query, sizeof query, "select label from %s.clade", cfgOption("central.db")); srDb = sqlGetResult(conn, query); while ((rowDb = sqlNextRow(srDb)) != NULL) { strcpy(clade, rowDb[0]); slNameAddTail(&list, clade); } sqlFreeResult(&srDb); return list; } struct blastTab* loadBlastpHits(struct sqlConnection *conn, char* queryName) /* Load all blastp hits of the given query gene into a list */ { char query[512]; struct sqlResult *srBlastpHits = NULL; struct blastTab *list = NULL; struct blastTab *blastpHits; char **row; char blastpHitsTable[] = "blastpHits"; if (hTableExists(database, blastpHitsTable)) { sqlSafef(query, sizeof query, "select * from %s where query = '%s'", blastpHitsTable, queryName); srBlastpHits = sqlGetResult(conn, query); while ((row = sqlNextRow(srBlastpHits)) != NULL) { blastpHits = blastTabLoad(row); slAddTail(&list, blastpHits); } } if (srBlastpHits != NULL) sqlFreeResult(&srBlastpHits); return list; } void printBlastpResult(struct sqlConnection *conn, struct blastTab *blastpHitsList, unsigned int querySeqLength) /* Print Blastp result of given clade */ { char query[512]; struct sqlResult *sr; char **row; char refSeq[50]; char xraTable[50]; char product[255]; struct blastTab *blastpHits; struct minGeneInfo *ginfo; char *blastpTarget[2]; char *clades[2]; int cladePortionCount = 0; char genome[50] = ""; char clade[50] = ""; unsigned int hitStart = 0; unsigned int hitEnd = 0; char **buffer = NULL; boolean findTable = FALSE; int tStart = cartInt(cart, "o"); int tEnd = cartInt(cart, "t"); char *tChrom = cartString(cart, "c"); printf("<br>\n"); /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 " "cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"18%%\"><b>Organism</b></td>\n"); printf("<td width=\"7%%\"><b>Clade</b></td>\n"); printf("<td width=\"7%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"5%%\"><b>Percent Length of Full Protein</b></td>\n"); printf("<td width=\"8%%\"><b>Position in Source Protein</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Identity (%%)</b></td>\n"); printf("<td width=\"5%%\"><b>E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Log of E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Bit Score</b></td>\n"); printf("<td width=\"6%%\"><b>Protein Alignment Length</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Mismatches</b></td>\n"); printf("<td width=\"5%%\"><b>Alignment Gaps</b></td>\n"); printf("</tr>\n"); blastpHits = blastpHitsList; while (blastpHits != NULL) { parseDelimitedString(blastpHits->target, ':', blastpTarget, 2); /* Get species info */ memset(genome, 0, 50); memset(clade, 0, 50); getGenomeClade(conn, blastpTarget[0], genome, clade); if ((strcmp(genome , "") != 0) && (strcmp(clade, "") != 0)) { cladePortionCount = parseDelimitedString(clade, '-', clades, 2); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td><a name=\"%s:%s:%u-%u\"><i>%s</i></td>\n", blastpTarget[1], tChrom, tStart, tEnd, genome); if (cladePortionCount == 1) printf("<td>%s</td>\n", clades[0]); else if (cladePortionCount == 2) printf("<td>%s<br>%s</td>\n", clades[0], clades[1]); /* Get target gene position from refSeq */ strcpy(refSeq, blastpTarget[0]); strcat(refSeq, "."); if (hDbExists(blastpTarget[0])) { if (hTableExists(blastpTarget[0], "lookup")) { sqlSafef(query, sizeof query, "select lookupValue from %s.lookup where lookupCode = 'annotRev'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcat(refSeq, row[0]); findTable = TRUE; sqlFreeResult(&sr); } } else if (hTableExists(blastpTarget[0], "refSeq")) { strcat(refSeq, "refSeq"); findTable = TRUE; } if (findTable) { sqlSafef(query, sizeof query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'", refSeq, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { hitStart = strtoul(row[1], buffer, 10) + blastpHits->tStart * 3 + 1; hitEnd = strtoul(row[1], buffer, 10) + blastpHits->tEnd * 3; printf("<td><a href=\"hgTracks\?position=%s:%u-%u&db=%s\" TARGET=_blank>%s</a></td>\n", row[0], hitStart, hitEnd, blastpTarget[0], blastpTarget[1]); } else printf("<td>%s</td>\n", blastpTarget[1]); sqlFreeResult(&sr); } else printf("<td>%s</td>\n", blastpTarget[1]); } else printf("<td>%s</td>\n", blastpTarget[1]); /* Get target gene product annotation */ if (hDbExists(blastpTarget[0])) { if (hTableExists(blastpTarget[0], "lookup")) { sqlSafef(query, sizeof query, "select lookupValue from %s.lookup where lookupCode = 'annotRevXra'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(xraTable, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); sqlSafef(query, sizeof query, "select product from %s.%s where name = '%s'", blastpTarget[0], xraTable, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(product, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); } else { ginfo = getGbProtCodeInfo(conn, blastpTarget[0], blastpTarget[1]); if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none")) strcpy(product, ginfo->product); else strcpy(product, "N/A"); } printf("<td>%s</td>\n", product); } else printf("<td>%s</td>\n", "N/A"); printf("<td style=\"text-align: center;\">%0.f</td>\n", ((double) (blastpHits->qEnd - blastpHits->qStart) / ((double) (querySeqLength-3) / 3.0f)) * 100.0f); printf("<td style=\"text-align: center;\">%u - %u</td>\n", blastpHits->qStart + 1, blastpHits->qEnd); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastpHits->identity); printf("<td style=\"text-align: right;\">%0.0e</td>\n", blastpHits->eValue); printf("<td style=\"text-align: right;\">e%0.0f</td>\n", (blastpHits->eValue == 0)? 0 : log(blastpHits->eValue) / log(10)); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastpHits->bitScore); printf("<td style=\"text-align: right;\">%u</td>\n", blastpHits->aliLength); printf("<td style=\"text-align: right;\">%u</td>\n", blastpHits->mismatch); printf("<td style=\"text-align: right;\">%u</td>\n", blastpHits->gapOpen); printf("</tr>\n"); } free(blastpTarget[0]); free(blastpTarget[1]); blastpHits = blastpHits->next; } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } void doBlastP(struct trackDb *tdb, char *targetName) /* Handle the BlastP Archaea and BlastP Bacteria tracks. */ { char queryName[50]; char queryTable[50]; unsigned int querySeqLength = 0; struct sqlConnection *conn = hAllocConn(database); struct bed *blastpTrack; struct blastTab *blastpHitsList; char query[512]; struct sqlResult *sr; char **row; cartWebStart(cart, database, "%s", "BlastP Alignment Hits"); blastpTrack = getBlastpTrackRecord(conn, tdb, targetName); if (hTableExists(database, "lookup")) { sqlSafef(query, sizeof query, "select lookupValue from lookup where lookupCode = 'annotRev'"); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(queryTable, row[0]); sqlFreeResult(&sr); } } else strcpy(queryTable, "refSeq"); printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength, queryTable); blastpHitsList = loadBlastpHits(conn, queryName); printBlastpResult(conn, blastpHitsList, querySeqLength); printf("<BR>Note: All measurements are counted by the number of amino acids.<BR>\n"); printf("<hr>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void doSelfHomologs(struct trackDb *tdb, char *targetName) /* Handle the Self Homologs tracks. */ { char queryName[50]; char queryTable[50]; unsigned int querySeqLength = 0; struct sqlConnection *conn = hAllocConn(database); struct bed *blastpTrack; struct blastTab *blastpHitsList; char query[512]; struct sqlResult *sr; char **row; cartWebStart(cart, database, "%s", "Homologs Within Genome by BlastP Search"); blastpTrack = getBlastpTrackRecord(conn, tdb, targetName); if (hTableExists(database, "lookup")) { sqlSafef(query, sizeof query, "select lookupValue from lookup where lookupCode = 'annotRev'"); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(queryTable, row[0]); sqlFreeResult(&sr); } } else strcpy(queryTable, "refSeq"); printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength, queryTable); blastpHitsList = loadSelfBlastpHits(conn, queryName, 1); printBlastpResult(conn, blastpHitsList, querySeqLength); printf("<BR>Note: All measurements are counted by the number of amino acids.<BR>\n"); printf("<hr>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void printQuerySequenceInfo(struct sqlConnection *conn, struct bed *blastxTrack, char *queryName, unsigned int *querySeqLength, char *queryTable) /* Get and print blastx query sequence info */ { char query[512]; struct sqlResult *srQuerySeq; char **row; int seqCount; char **buffer = NULL; char *targetGeneName[2]; char blastxHits[] = "blastxHits"; unsigned int queryStart = 0; unsigned int queryEnd = 0; parseDelimitedString(blastxTrack->name, ':', targetGeneName, 2); if (hTableExists(database, queryTable) && hTableExists(database, blastxHits)) { /* Get query sequence from query table */ sqlSafef(query, sizeof query, "select count(*) from %s where chrom = '%s' and chromStart <= %u and chromEnd >= %u", queryTable, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); srQuerySeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srQuerySeq)) != NULL) { seqCount = atoi(row[0]); sqlFreeResult(&srQuerySeq); if (seqCount == 1) { sqlSafef(query, sizeof query, "select name, chromStart, chromEnd from %s where chrom = '%s' and chromStart <= %u and chromEnd >= %u", queryTable, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); srQuerySeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srQuerySeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srQuerySeq); } else { /* Check blastxHits if more than 1 query sequence is found within the region */ sqlSafef(query, sizeof query, "select a.name, a.chromStart, a.chromEnd from %s a, %s b where a.chrom = '%s' and a.chromStart <= %u and a.chromEnd >= %u and a.name = b.query and b.target like '%%%s'", queryTable, blastxHits, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd, targetGeneName[0]); srQuerySeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srQuerySeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srQuerySeq); } if ((queryStart == 0) && (queryEnd == 0)) printf("Query sequence not found for %s at %s:%u-%u\n", blastxTrack->name, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); else { *querySeqLength = (blastxTrack->chromEnd - blastxTrack->chromStart); /* Print query sequence info */ printf("<B>Query sequence: </B>%s<BR>\n", queryName); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, blastxTrack->chrom, queryStart + 1, queryEnd); printf("%s:%d-%d</A><BR>\n", blastxTrack->chrom, queryStart + 1, queryEnd); printf("<B>Genomic size: </B> %d nt<BR><BR>\n", (queryEnd - queryStart)); printf("<B>BlastX hit position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, blastxTrack->chrom, blastxTrack->chromStart + 1, blastxTrack->chromEnd); printf("%s:%d-%d</A><BR>\n", blastxTrack->chrom, blastxTrack->chromStart + 1, blastxTrack->chromEnd); printf("<B>BlastX hit position relative to query sequence: </B> %d-%d<BR>\n", blastxTrack->chromStart - queryStart + 1, blastxTrack->chromEnd - queryStart); printf("<B>BlastX hit genomic size: </B> %d nt<BR>\n", (blastxTrack->chromEnd - blastxTrack->chromStart)); } } else printf("<BR>Query sequence not found for %s at %s:%u-%u<BR>\n", blastxTrack->name, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); } sqlFreeResult(&srQuerySeq); free(targetGeneName[0]); free(targetGeneName[1]); } struct blastTab* loadBlastxHits(struct sqlConnection *conn, char* queryName, char* queryTable, struct bed *blastxTrack) /* Load all blastx hits of the given query region into a list */ { char query[512]; struct sqlResult *srBlastxHits = NULL; struct blastTab *list = NULL; struct blastTab *blastxHits; struct sqlResult *srQuery = NULL; struct bed *queryTrack = NULL; char **rowQuery; int rowOffset; char **row; char blastxHitsTable[] = "blastxHits"; unsigned int queryStart = 0; unsigned int queryEnd = 0; unsigned int qStart = 0; unsigned int qEnd = 0; if (hTableExists(database, queryTable) && hTableExists(database, blastxHitsTable)) { rowOffset = hOffsetPastBin(database, seqName, queryTable); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", queryTable, queryName); srQuery = sqlGetResult(conn, query); if ((rowQuery = sqlNextRow(srQuery)) != NULL) { queryTrack = bedLoadN(rowQuery+rowOffset, 6); queryStart = blastxTrack->chromStart - queryTrack->chromStart + 1; queryEnd = blastxTrack->chromEnd - queryTrack->chromStart; } sqlFreeResult(&srQuery); srQuery = NULL; sqlSafef(query, sizeof query, "select * from %s where query = '%s'", blastxHitsTable, queryName); srBlastxHits = sqlGetResult(conn, query); while ((row = sqlNextRow(srBlastxHits)) != NULL) { blastxHits = blastTabLoad(row); if (blastxHits->qStart < blastxHits->qEnd) { qStart = blastxHits->qStart; qEnd = blastxHits->qEnd; } else { qStart = blastxHits->qEnd; qEnd = blastxHits->qStart; } if (((qStart <= queryStart) && (qEnd >= queryEnd)) || ((qStart >= queryStart) && (qStart <= queryEnd)) || ((qEnd >= queryStart) && (qEnd <= queryEnd))) slAddTail(&list, blastxHits); } } if (srQuery != NULL) sqlFreeResult(&srQuery); if (srBlastxHits != NULL) sqlFreeResult(&srBlastxHits); return list; } void printBlastxResult(struct sqlConnection *conn, struct blastTab *blastxHitsList, unsigned int querySeqLength) /* Print Blastx result of given clade */ { char query[512]; struct sqlResult *sr; char **row; char refSeq[50]; struct blastTab *blastxHits; struct minGeneInfo *ginfo; char *blastxTarget[2]; char *clades[2]; int cladePortionCount = 0; char genome[50] = ""; char clade[50] = ""; unsigned int targetProteinStart = 0; unsigned int targetProteinEnd = 0; unsigned int hitStart = 0; unsigned int hitEnd = 0; char **buffer = NULL; int tStart = cartInt(cart, "o"); int tEnd = cartInt(cart, "t"); char *tChrom = cartString(cart, "c"); printf("<br>\n"); /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 " "cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"10%%\"><b>Organism</b></td>\n"); printf("<td width=\"7%%\"><b>Clade</b></td>\n"); printf("<td width=\"7%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"7%%\"><b>Position in Query Genomic Sequence</b></td>\n"); printf("<td width=\"7%%\"><b>Position in Target Protein</b></td>\n"); printf("<td width=\"7%%\"><b>Percent Length of Target Protein</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Identity (%%)</b></td>\n"); printf("<td width=\"5%%\"><b>E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Log of E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Bit Score</b></td>\n"); printf("<td width=\"8%%\"><b>Protein Alignment Length</b></td>\n"); printf("<td width=\"8%%\"><b>Protein Mismatches</b></td>\n"); printf("<td width=\"8%%\"><b>Alignment Gaps</b></td>\n"); printf("</tr>\n"); blastxHits = blastxHitsList; while (blastxHits != NULL) { parseDelimitedString(blastxHits->target, ':', blastxTarget, 2); /* Get species info */ memset(genome, 0, 50); memset(clade, 0, 50); getGenomeClade(conn, blastxTarget[0], genome, clade); if ((strcmp(genome , "") != 0) && (strcmp(clade, "") != 0)) { cladePortionCount = parseDelimitedString(clade, '-', clades, 2); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td><a name=\"%s:%s:%u-%u\"><i>%s</i></td>\n", blastxTarget[1], tChrom, tStart, tEnd, genome); if (cladePortionCount == 1) printf("<td>%s</td>\n", clades[0]); else if (cladePortionCount == 2) printf("<td>%s<br>%s</td>\n", clades[0], clades[1]); /* Get target gene position from refSeq */ strcpy(refSeq, blastxTarget[0]); strcat(refSeq, ".refSeq"); if (hDbExists(blastxTarget[0]) && hTableExists(blastxTarget[0], "refSeq")) { sqlSafef(query, sizeof query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'", refSeq, blastxTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { targetProteinStart = strtoul(row[1], buffer, 10); targetProteinEnd = strtoul(row[2], buffer, 10); hitStart = targetProteinStart + blastxHits->tStart * 3 + 1; hitEnd = targetProteinStart + blastxHits->tEnd * 3; printf("<td><a href=\"hgTracks\?position=%s:%u-%u&db=%s\" TARGET=_blank>%s</a></td>\n", row[0], hitStart, hitEnd, blastxTarget[0], blastxTarget[1]); } else printf("<td>%s</td>\n", blastxTarget[1]); sqlFreeResult(&sr); } else printf("<td>%s</td>\n", blastxTarget[1]); /* Get target gene product annotation */ if (hDbExists(blastxTarget[0])) { ginfo = getGbProtCodeInfo(conn, blastxTarget[0], blastxTarget[1]); if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none")) printf("<td>%s</td>\n", ginfo->product); else printf("<td>%s</td>\n", "N/A"); } else printf("<td>%s</td>\n", "N/A"); printf("<td style=\"text-align: center;\">%u - %u</td>\n", blastxHits->qStart + 1, blastxHits->qEnd); printf("<td style=\"text-align: center;\">%u - %u</td>\n", blastxHits->tStart + 1, blastxHits->tEnd); if ((targetProteinStart == 0) || (targetProteinEnd == 0)) printf("<td style=\"text-align: center;\">N/A</td>\n"); else printf("<td style=\"text-align: center;\">%0.f</td>\n", ((double) (blastxHits->tEnd - blastxHits->tStart) / ((double) (targetProteinEnd-targetProteinStart-3) / 3.0f)) * 100.0f); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastxHits->identity); printf("<td style=\"text-align: right;\">%0.0e</td>\n", blastxHits->eValue); printf("<td style=\"text-align: right;\">e%0.0f</td>\n", (blastxHits->eValue == 0)? 0 : log(blastxHits->eValue) / log(10)); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastxHits->bitScore); printf("<td style=\"text-align: right;\">%u</td>\n", blastxHits->aliLength); printf("<td style=\"text-align: right;\">%u</td>\n", blastxHits->mismatch); printf("<td style=\"text-align: right;\">%u</td>\n", blastxHits->gapOpen); printf("</tr>\n"); } free(blastxTarget[0]); free(blastxTarget[1]); blastxHits = blastxHits->next; } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } void doBlastX(struct trackDb *tdb, char *targetName) /* Handle the BlastX Archaea and BlastX Bacteria tracks. */ { char queryName[50]; char queryTable[50]; unsigned int querySeqLength = 0; struct sqlConnection *conn = hAllocConn(database); struct bed *blastxTrack; struct blastTab *blastxHitsList; cartWebStart(cart, database, "%s", "BlastX Alignment Hits"); blastxTrack = getBlastpTrackRecord(conn, tdb, targetName); /* if (!differentWord(blastxTrack->chrom, "assembly"))*/ if (hTableExists(database, "scaffolds")) strcpy(queryTable, "scaffolds"); else strcpy(queryTable, "igenics"); printQuerySequenceInfo(conn, blastxTrack, queryName, &querySeqLength, queryTable); blastxHitsList = loadBlastxHits(conn, queryName, queryTable, blastxTrack); printBlastxResult(conn, blastxHitsList, querySeqLength); printf("<BR>\n"); printf("<hr>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void doUltraConserved(struct trackDb *tdb, char *item) /* Handle the ultraConserved track. */ { char tableName[65]; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct hashEl* hashItem; struct hashCookie cookie; struct trackDb *multizTrack; struct sqlConnection *conn = hAllocConn(database); cookie = hashFirst(trackHash); hashItem = hashNext(&cookie); while (hashItem != NULL) { memset(tableName, 0, 65); strcpy(tableName, hashItem->name); if (strstr(tableName, "multiz") != NULL) break; hashItem = hashNext(&cookie); } multizTrack = hashFindVal(trackHash, tableName); winStart = start; winEnd = end; genericHeader(tdb, NULL); if (tdb->html != NULL && tdb->html[0] != 0) { puts(tdb->html); htmlHorizontalLine(); } genericMafClick(conn, multizTrack, item, start); printTrackHtml(multizTrack); hFreeConn(&conn); } float computeMolecularWeight(char* dna, int length) { float weight = 0.0f; int count[4] = {0,0,0,0}; int i = 0; for (i = 0; i < length; i++) { if ((dna[i] == 'A') || (dna[i] == 'a')) count[0]++; else if ((dna[i] == 'C') || (dna[i] == 'c')) count[1]++; else if ((dna[i] == 'G') || (dna[i] == 'g')) count[2]++; else if ((dna[i] == 'T') || (dna[i] == 't')) count[3]++; } weight = count[0] * 313.209 + count[1] * 289.184 + count[2] * 329.208 + count[3] * 304.196 - 63.980 + 2.016; return weight; } float computeNMolePerOD(char* dna, int length) { int extCoeff = 0; float nmolePerOD = 0.0f; enum { baseA = 0, baseC, baseG, baseT }; int indExtCoeff[4] = {15400, 7400, 11500, 8700}; int neighborExtCoeff[4][4] = { {27400, 21200, 25000, 22800}, {21200, 14600, 18000, 15200}, {25200, 17600, 21600, 20000}, {23400, 16200, 19000, 16800}}; int i = 0; int *bases = malloc(sizeof(int) * length); for (i = 0; i < length; i++) { if ((dna[i] == 'A') || (dna[i] == 'a')) bases[i] = baseA; else if ((dna[i] == 'C') || (dna[i] == 'c')) bases[i] = baseC; else if ((dna[i] == 'G') || (dna[i] == 'g')) bases[i] = baseG; else if ((dna[i] == 'T') || (dna[i] == 't')) bases[i] = baseT; } for (i = 0; i < (length - 1); i++) extCoeff += neighborExtCoeff[bases[i]][bases[i + 1]]; for (i = 1; i < (length - 1); i++) extCoeff -= indExtCoeff[bases[i]]; nmolePerOD = pow(10, 6) / (float) extCoeff; free(bases); return nmolePerOD; } void doPrimers(struct trackDb *tdb, char *primerName) /* Handle the array primer and GOLD primer tracks. */ { struct bed *primer; struct dnaSeq *sequence; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; int pairCount = 0; boolean forwardPrimer = TRUE; genericHeader(tdb, primerName); if (startsWith("Asn", primerName)) forwardPrimer = FALSE; dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, primerName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { primer = bedLoadN(row+rowOffset, bedSize); printf("<B>Primer name: </B> %s<BR>\n",primerName); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, primer->chrom, primer->chromStart + 1, primer->chromEnd); printf("%s:%d-%d</A><BR>\n", primer->chrom, primer->chromStart + 1, primer->chromEnd); printf("<B>Strand:</B> %s<BR>\n", primer->strand); printf("<B>Genomic size:</B> %d nt<BR><BR>\n", (primer->chromEnd - primer->chromStart)); sequence = hDnaFromSeq(database, primer->chrom, primer->chromStart, primer->chromEnd, dnaUpper); if (sequence != NULL) { if (strcmp(primer->strand, "-") == 0) reverseComplement(sequence->dna, sequence->size); printf("<B>Sequence:</B> 5' %s 3'<BR>\n", sequence->dna); printf("<B>GC content:</B> %0.2f%%<BR>\n", computeGCContent(sequence->dna, sequence->size)); printf("<B>Molecular weight:</B> %0.1f g/mol<BR>\n", computeMolecularWeight(sequence->dna, sequence->size)); printf("<B>nmole/OD<sub>260</sub>:</B> %0.3f <BR>\n", computeNMolePerOD(sequence->dna, sequence->size)); printf("<B>ug/OD<sub>260</sub>:</B> %0.3f <BR>\n", computeNMolePerOD(sequence->dna, sequence->size) * computeMolecularWeight(sequence->dna, sequence->size) * pow(10,-3)); } if (primer->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>Primer pairing</B><br>\n"); /* Print table */ printf("<table style=\"width: 90%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 " "cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"20%%\"><b>Primer Name</b></td>\n"); printf("<td width=\"10%%\"><b>Primer Type</b></td>\n"); printf("<td width=\"30%%\"><b>Primer Sequence</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Region</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Length (bp)</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Region<BR>GC Content (%%)</b></td>\n"); printf("</tr>\n"); memset(query, 0, 512); if (strcmp(primer->strand, "+") == 0) { if (hTableExists(database, "genomePcrPrimers")) sqlSafef(query, sizeof query, "select *, 'Array PCR' primerType from genomePcrPrimers where chrom = '%s' and chromStart > %d and strand = '-'", primer->chrom, primer->chromEnd); if (hTableExists(database, "goldRTprimers")) { if (strcmp(query, "") != 0) sqlSafef(query, sizeof query, "%s union ", query); sqlSafef(query, sizeof query, "%sselect *, 'GOLD RT' primerType from goldRTprimers where chrom = '%s' and chromStart > %d and strand = '-'", query, primer->chrom, primer->chromEnd); } sqlSafef(query, sizeof query, "%s order by chromStart", query); } else { if (hTableExists(database, "genomePcrPrimers")) sqlSafef(query, sizeof query, "select *, 'Array PCR' primerType from genomePcrPrimers where chrom = '%s' and chromEnd < %d and strand = '+'", primer->chrom, primer->chromStart); if (hTableExists(database, "goldRTprimers")) { if (strcmp(query, "") != 0) sqlSafef(query, sizeof query, "%s union ", query); sqlSafef(query, sizeof query, "%sselect *, 'GOLD RT' primerType from goldRTprimers where chrom = '%s' and chromEnd < %d and strand = '+'", query, primer->chrom, primer->chromStart); } sqlSafef(query, sizeof query, "%s order by chromStart desc", query); } sr = sqlGetResult(conn, query); while (((row = sqlNextRow(sr)) != NULL) && (pairCount < 6)) { if ((forwardPrimer && startsWith("Asn", row[4])) || (!forwardPrimer && startsWith("Sn", row[4]))) { printf("<tr style=\"vertical-align: top;\">\n"); printf("<td>" "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, row[1], atoi(row[2]) + 1, atoi(row[3])); printf("%s</A></td>\n", row[4]); printf("<td>%s</td>\n", row[7]); sequence = hDnaFromSeq(database, row[1], atoi(row[2]), atoi(row[3]), dnaUpper); if (sequence != NULL) { if (strcmp(row[6], "-") == 0) reverseComplement(sequence->dna, sequence->size); printf("<td>5' %s 3'</td>\n", sequence->dna); } else printf("<td>N/A</td>\n"); if (strcmp(primer->strand, "+") == 0) { sequence = hDnaFromSeq(database, primer->chrom, primer->chromStart, atoi(row[3]), dnaUpper); printf("<td>" "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, primer->chrom, primer->chromStart + 1, atoi(row[3])); printf("%s:%d-%d</A></td>\n", primer->chrom, primer->chromStart + 1, atoi(row[3])); } else { sequence = hDnaFromSeq(database, primer->chrom, atoi(row[2]), primer->chromEnd, dnaUpper); printf("<td>" "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, primer->chrom, atoi(row[2]) + 1, primer->chromEnd); printf("%s:%d-%d</A></td>\n", primer->chrom, atoi(row[2])+ 1, primer->chromEnd); } if (sequence != NULL) { printf("<td style=\"text-align: right;\">%d</td>\n", sequence->size); printf("<td style=\"text-align: right;\">%0.2f</td>\n", computeGCContent(sequence->dna, sequence->size)); } else { printf("<td>N/A</td>\n"); printf("<td>N/A</td>\n"); } printf("</tr>\n"); pairCount++; } } sqlFreeResult(&sr); /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); bedFree(&primer); hFreeConn(&conn); printTrackHtml(tdb); } void doWiki(char *track, struct trackDb *tdb, char *itemName) { char strand[2]; printf("<HEAD>"); if(startsWith("Make", itemName)) { strand[0] = itemName[strlen(itemName)-1]; strand[1] = 0; printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.cse.ucsc.edu/index.php/BED:%s:%s:%d-%d:%s\"</META>", database, seqName, winStart, winEnd, strand); } else { printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.cse.ucsc.edu/index.php/BED:%s:%s:%s\"</META>", database, seqName, itemName); } printf("</HEAD>"); } void doRNAHybridization(struct trackDb *tdb, char *itemName) { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; struct rnaHybridization *rnaHyb; char rnaHybridizationTable[] = "rnaHybridization"; char tRNATable[] = "tRNAs"; char jgiTable[] = "jgiGene"; char *saveTableName; int i; cartWebStart(cart, database, "%s", "RNAHybridization Sites"); if (hTableExists(database, rnaHybridizationTable)) { /* Get query gene from refSeq */ sqlSafef(query, sizeof query, "select * from %s where name='%s'", rnaHybridizationTable, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { rnaHyb = rnaHybridizationLoad(row); printf("<b>Hybridization Site:</b><br/><br/>"); /* print hybridization site */ printf("<span style='font-family:Courier;'>"); printf("Pattern 5%s3<br>", rnaHyb->patternSeq); printf("         "); for(i=0;i<rnaHyb->matchLength;i++) printf("|"); printf("<br/>"); printf("Target  3%s5", rnaHyb->targetSeq); printf("</span><br/><br/>"); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",rnaHyb->matchLength); printf("<b>Percentage G-C base-pairs:</b> %d<br/>", (int)(rnaHyb->gcContent * 100)); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("%s:%d-%d</A><BR>\n", rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("<B>Strand:</B> %s<BR>\n", rnaHyb->strand); printf("<B>Target Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); printf("%s:%d-%d</A><BR>\n", rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); printf("<B>Target Strand:</B> %s<BR>\n", rnaHyb->strandTarget); printf("<br/>"); if(strlen(rnaHyb->refSeqTarget) > 0) { printf("<b>Additional information for target<b><br/>"); printf("<hr/>"); doRefSeq(tdb, rnaHyb->refSeqTarget,"gbProtCodePep","gbProtCodeXra"); } if(strlen(rnaHyb->JGITarget) > 0) { saveTableName = tdb->table; tdb->table = jgiTable; printf("<b>Additional information for target<b><br/>"); printf("<hr/>"); doJgiGene(tdb, rnaHyb->JGITarget); tdb->table = saveTableName; } if(strlen(rnaHyb->trnaTarget) > 0) { saveTableName = tdb->table; tdb->table = tRNATable; printf("<b>Additional information for target<b><br/>"); printf("<hr/>"); doTrnaGenes(tdb, rnaHyb->trnaTarget); tdb->table = saveTableName; } freeMem(rnaHyb); } sqlFreeResult(&sr); } hFreeConn(&conn); } void doarCOGs(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct arCOGs *infoload; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); sqlSafef(query, sizeof query, "select * from mgCommonDb.arcogdesc where name = '%s'", itemName); //sqlSafef(query, sizeof query, "select * from %s where query = '%s'", blastpHitsTable, queryName); struct sqlResult *srarcogdesc = sqlGetResult(conn, query); struct arcogdesc *description = NULL; while ((row = sqlNextRow(srarcogdesc)) != NULL) { struct arcogdesc *element; element = arcogdescLoad(row); slAddTail(&description, element); } sqlFreeResult(&srarcogdesc); genericHeader(tdb,itemName); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = arCOGsLoad(row+rowOffset); printf("<B>Name:</B> %s<BR>\n", infoload->name); printf("<B>Description:</B> %s<BR>\n", description->description); printf("<B>Code:</B> %s<BR>\n", description->code); printf("<B>Gene:</B> %s<BR>\n", infoload->gene); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); arCOGsFree(&infoload); printTrackHtml(tdb); } void doloweOrthologs(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct bed *infoload; int bedSize = 0; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = bedLoadN(row+rowOffset, bedSize); printf("<B>Name:</B> %s\n", infoload->name); printf(" <A HREF=\"http://archdev-holmes.cse.ucsc.edu/cgi-bin/hgFrame?track=loweOrthologs&refseq=1&db=%s&name=%s\">List of Orthologs</A><BR>",database,infoload->name); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doCddInfo(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct cddInfo *infoload; int bedSize = 0; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; sqlSafef(query, sizeof query, "select * from mgCommonDb.cddDesc where accession = '%s'", itemName); //sqlSafef(query, sizeof query, "select * from %s where query = '%s'", blastpHitsTable, queryName); struct sqlResult *srCddDesc = sqlGetResult(conn, query); struct cddDesc *description = NULL; while ((row = sqlNextRow(srCddDesc)) != NULL) { struct cddDesc *element; element = cddDescLoad(row); slAddTail(&description, element); } sqlFreeResult(&srCddDesc); genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = cddInfoLoad(row+rowOffset); printf("<B>Name:</B> %s<BR>\n", infoload->fullname); printf("<B>Accession:</B> %s<A HREF=\"http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s\" TARGET=_blank>", infoload->name, infoload->NCBInum); printf(" Link to NCBI Site</A> <BR>\n"); printf("<B>E-value:</B> %0.0e<BR>\n", infoload->evalue); printf("<B>Description:</B> %s<BR>\n", description->name); printf("<B>Protein Identity:</B> %u%%<BR>\n", infoload->percentident); printf("<B>Percent Length:</B> %u%%<BR>\n", infoload->percentlength); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); cddInfoFree(&infoload); printTrackHtml(tdb); } void domegablastInfo(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct megablastInfo *infoload; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb,itemName); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = megablastInfoLoad(row+rowOffset); printf("<B>Name:</B> %s<BR>\n", infoload->name); printf("<B>Accession:</B> %s<A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/%s\" TARGET=_blank>", infoload->name, infoload->name); printf(" Link to NCBI Site</A> <BR>\n"); printf("<B>Description:</B> %s<BR>\n", infoload->fullname); printf("<B>E-value:</B> %0.0e", infoload->evalue); #ifdef LISTUI printf(" <A HREF=\"http://archdev-holmes.cse.ucsc.edu/cgi-bin/hgList?track=megablastInfo&order=evalue&db=%s\">Sort by E-value</A>",database); #endif printf("<BR>\n"); printf("<B>Protein Identity:</B> %u%%\n", infoload->percentident); #ifdef LISTUI printf(" <A HREF=\"http://archdev-holmes.cse.ucsc.edu/cgi-bin/hgList?track=megablastInfo&order=percentident&db=%s\">Sort by Percent Identity</A>",database); #endif printf("<BR>\n"); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); megablastInfoFree(&infoload); printTrackHtml(tdb); } void doAlignInfo(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct alignInfo *infoload; int bedSize = 0; int start = cartInt(cart, "o"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d;", tdb->table, itemName,seqName,start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = alignInfoLoad(row+rowOffset); printf("<B>Name:</B> %s ", infoload->name); linkToOtherBrowserTitle(infoload->orgn, infoload->alignChrom, infoload->alignChromStart + 1, infoload->alignChromEnd, "Aligned Feature"); //printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", //hgTracksPathAndSettings(), infoload->orgn, infoload->alignChrom, infoload->alignChromStart + 1, infoload->alignChromEnd); printf("Link to Feature</A><BR>\n" ); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); break; } sqlFreeResult(&sr); hFreeConn(&conn); alignInfoFree(&infoload); printTrackHtml(tdb); } void doCRISPRs(struct trackDb *tdb, char *crisprName) /* Handle the CRISPR array track. */ { struct bed *crispr; struct dnaSeq *sequence; char tempSeq[512]; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; int pairCount = 0; genericHeader(tdb, crisprName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, ArraySize(query), "select * from %s where name = '%s'", tdb->table, crisprName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { crispr = bedLoadN(row+rowOffset, bedSize); printf("<B>Name: </B> %s<BR>\n", crisprName); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("%s:%d-%d</A><BR>\n", crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("<B>Strand:</B> %s<BR>\n", crispr->strand); printf("<B>Genomic size:</B> %d nt<BR><BR>\n", (crispr->chromEnd - crispr->chromStart)); printf("<B>Number of spacers:</B> %u<BR><BR>\n", crispr->blockCount - 1); sequence = hDnaFromSeq(database, crispr->chrom, crispr->chromStart, crispr->chromEnd, dnaUpper); if (sequence != NULL) { /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' " "border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td colspan=\"3\"><b>Direct Repeat</b></td>\n"); printf("<td colspan=\"3\"><b>Spacer</b></td>\n"); printf("</tr>\n"); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"8%%\"><b>Start Pos</b></td>\n"); printf("<td width=\"36%%\"><b>Sequence</b></td>\n"); printf("<td width=\"4%%\"><b>Length</b></td>\n"); printf("<td width=\"8%%\"><b>Start Pos</b></td>\n"); printf("<td><b>Sequence</b></td>\n"); printf("<td width=\"4%%\"><b>Length</b></td>\n"); printf("</tr>\n"); if (strcmp(crispr->strand, "+") == 0) { for (pairCount = 0; pairCount < (int) crispr->blockCount; pairCount++) { printf("<tr style=\"vertical-align: top;\">\n"); memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount], crispr->blockSizes[pairCount]); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + 1 + crispr->chromStarts[pairCount], tempSeq, crispr->blockSizes[pairCount]); if (pairCount + 1 < crispr->blockCount) { memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], crispr->chromStarts[pairCount+1] - crispr->blockSizes[pairCount] - crispr->chromStarts[pairCount]); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + 1 + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], tempSeq, crispr->chromStarts[pairCount+1] - crispr->blockSizes[pairCount] - crispr->chromStarts[pairCount]); } else { printf("<td> </td><td> </td><td> </td>\n"); } printf("</tr>\n"); } } else { for (pairCount = ((int)crispr->blockCount - 1); pairCount >= 0; pairCount--) { printf("<tr style=\"vertical-align: top;\">\n"); memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount], crispr->blockSizes[pairCount]); reverseComplement(tempSeq, strlen(tempSeq)); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], tempSeq, crispr->blockSizes[pairCount]); if (pairCount - 1 >= 0) { memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount-1] + crispr->blockSizes[pairCount-1], crispr->chromStarts[pairCount] - crispr->blockSizes[pairCount-1] - crispr->chromStarts[pairCount-1]); reverseComplement(tempSeq, strlen(tempSeq)); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + crispr->chromStarts[pairCount], tempSeq, crispr->chromStarts[pairCount] - crispr->blockSizes[pairCount-1] - crispr->chromStarts[pairCount-1]); } else { printf("<td> </td><td> </td><td> </td>\n"); } printf("</tr>\n"); } } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } if (crispr->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); bedFree(&crispr); hFreeConn(&conn); printTrackHtml(tdb); } bool loweLabClick(char *track, char *item, struct trackDb *tdb) /* check if we have one of the lowelab tracks */ { if (endsWith(track, "PgSnp")) { doPgSnp(tdb, item, NULL); } else if (sameWord(track, "gbProtCode")) { llDoCodingGenes(tdb, item,"gbProtCodePep","gbProtCodeXra"); } else if (sameWord(track, "refSeq")) { doRefSeq(tdb, item,"gbProtCodePep","gbProtCodeXra"); } else if (startsWith("annotRev", track)) { doRefSeq(tdb, item,"Pep","Xra"); } else if (sameWord(track, "sargassoSea")) { doSargassoSea(tdb, item); } else if (sameWord(track, "tigrCmrORFs")) { doTigrCmrGene(tdb,item); } else if (sameWord(track, "jgiGene")) { doJgiGene(tdb,item); } else if (sameWord(track, "lowelabPfamHits")) { doPfamHit(tdb,item); } /*else if (sameWord(track, "tigrOperons"))*/ else if (sameWord(track, "lowelabTIGROperons")) { doTigrOperons(tdb,item); } else if (sameWord(track, "lowelabArkinOperons")) { doArkinOperons(tdb,item); } else if (sameWord(track,"codeBlast")) { doCodeBlast(tdb, item); } else if (sameWord(track,"gbRNAs")) { doGbRnaGenes(tdb, item); } else if (sameWord(track,"tRNAs")) { doTrnaGenes(tdb, item); } else if (sameWord(track,"snoRNAs")) { doSnornaGenes(tdb, item); } else if (sameWord(track,"easyGene")) { doEasyGenes(tdb, item); } else if (startsWith("BlastP_", track) && differentWord(track, "BlastP_Crenarchaea") && differentWord(track, "BlastP_Nanoarch") && differentWord(track, "BlastP_Euryarch") && differentWord(track, "BlastP_Bacteria")) { doBlastP(tdb, item); } else if (startsWith("BlastX_", track) && differentWord(track, "BlastX_Crenarchaea") && differentWord(track, "BlastX_Nanoarch") && differentWord(track, "BlastX_Euryarch") && differentWord(track, "BlastX_Bacteria")) { doBlastX(tdb, item); } else if (sameWord(track,"ultraConserved")) { doUltraConserved(tdb, item); } else if (sameWord(track,"genomePcrPrimers") || sameWord(track,"goldRTPrimers")) { doPrimers(tdb, item); } else if (sameWord(track,"wiki") || sameWord(track,"wikibme")) { doWiki(track,tdb,item); } else if (sameWord(track,"rnaHybridization")) { doRNAHybridization(tdb, item); } else if (sameWord(track,"cddInfo")) { doCddInfo(tdb, item); } else if (sameWord(track,"alignInfo")) { doAlignInfo(tdb, item); } else if (sameWord(track,"arCOGs")) { doarCOGs(tdb, item); } else if (sameWord(track,"megablastInfo") || sameWord(track,"vecScreenInfo")) { domegablastInfo(tdb, item); } else if (sameWord(track,"loweOrthologs")) { doloweOrthologs(tdb, item); } else if (sameWord(track,"selfHomologs")) { doSelfHomologs(tdb, item); } else if (sameWord(track,"CRISPRs")) { doCRISPRs(tdb, item); } else return FALSE; return TRUE; }