314b81670d2d1446d4da81108ac0ce2a72fc569d markd Fri Jan 6 15:32:57 2017 -0800 bigTransMap hgc working diff --git src/hg/hgc/transMapClick.c src/hg/hgc/transMapClick.c index 827e019..92a70b3 100644 --- src/hg/hgc/transMapClick.c +++ src/hg/hgc/transMapClick.c @@ -1,265 +1,341 @@ /* transMapClick - transMap click handling */ /* Copyright (C) 2010 The Regents of the University of California * See README in this or parent directory for licensing information. */ +/* FIXME: the two version support should be be delete once support + * for table version is fully dropped. + */ + /* + * For the older table-based version of transMap, the following + * tables are used. These are mapped into the bigTransMap objects. + * * Per-genome tables associated with transMap: * transMapAliXxx - mapped PSLs alignments * transMapInfoXxx - information for mapped alignments * hgFixed tables associated with transMap: * transMapSrcXxx - information about source alignments * transMapGeneXxx - gene information * transMapSeqXxx - seq table for accessing sequence * transMapExtFileXxx - extFile table * * Xxx is: * - UcscGene - UCSC genes * - RefSeq - RefSeq mRNAs * - MRna - GenBank mRNAs * - SplicedEst - GenBank spliced ESTs */ #include "common.h" #include "hgc.h" #include "hui.h" #include "hCommon.h" #include "transMapClick.h" +#include "bigTransMap.h" +#include "bigBed.h" +#include "bigPsl.h" #include "transMapStuff.h" #include "transMapInfo.h" #include "transMapSrc.h" #include "transMapGene.h" #include "genbank.h" struct transMapBag -/* object contain collected information on a specific transMap mapping */ +/* object contain collected information on a specific transMap mapping +* this has both PSL and bigTransMap objects */ { struct psl *psl; // transMap alignment - struct transMapInfo *info; // addition information about mapping - struct transMapSrc *src; // source information - struct transMapGene *gene; // gene information + struct bigTransMap *meta; // bigTransMap record for metadata boolean srcDbIsActive; // source database is active }; -static struct transMapBag *transMapBagLoad(struct sqlConnection *conn, - struct trackDb *tdb, char *mappedId, - boolean getSrcRec) -/* load information from various tables */ +static char *guessTranscriptType(struct transMapGene *gene) +/* guess the transcript type when not known */ +{ +if (gene == NULL) + return "unknown"; // EST +else if (sameString(gene->cds, "n/a") || sameString(gene->cds, "")) + return "non_coding"; +else + return "protein_coding"; +} + +static char *chainSubsetToBigStr(enum transMapInfoChainSubset cs) +/* convert chain subset type to string used in bigTransMap */ { +switch (cs) + { + case transMapInfoUnknown: + assert(FALSE); + return "unknown"; + case transMapInfoAll: + return "all"; + case transMapInfoSyn: + return "syn"; + case transMapInfoRbest: + return "rbest"; + } +assert(FALSE); +return NULL; +} + +static struct bigTransMap *buildFakeBigTransMapRec(struct transMapInfo *info, + struct transMapSrc *src, + struct transMapGene *gene) +/* build a partial bigTransMap record from the tables; only metadata fields + * are filled in. */ +{ +struct bigTransMap *bigTransMap; +AllocVar(bigTransMap); +bigTransMap->seqType = 1; +bigTransMap->srcDb = cloneString(src->db); +bigTransMap->srcChrom = cloneString(src->chrom); +bigTransMap->srcChromStart = src->chromStart; +bigTransMap->srcChromEnd = src->chromEnd; +bigTransMap->srcScore = (int)(1000.0*src->ident); +bigTransMap->srcAligned = (int)(1000.0*src->aligned); +if (gene != NULL) + { + bigTransMap->geneName = cloneString(gene->geneName); + bigTransMap->geneId = cloneString(gene->geneId); + } +bigTransMap->geneType = cloneString(guessTranscriptType(gene)); // set for ESTs +bigTransMap->transcriptType = cloneString(guessTranscriptType(gene)); +bigTransMap->chainType = cloneString(chainSubsetToBigStr(info->chainSubset)); +bigTransMap->commonName = hOrganism(info->srcDb); +if (bigTransMap->commonName == NULL) + bigTransMap->commonName = cloneString(""); +bigTransMap->orgAbbrev = cloneString(emptyForNull(hOrgShortForDb(info->srcDb))); +return bigTransMap; +} + +static struct transMapBag *transMapBagLoadDb(struct trackDb *tdb, char *mappedId) +/* load information from various tables for database version of transmap */ +{ +struct sqlConnection *conn = hAllocConn(database); struct transMapBag *bag; AllocVar(bag); bag->psl = getAlignments(conn, tdb->table, mappedId); char *transMapInfoTbl = trackDbRequiredSetting(tdb, transMapInfoTblSetting); -bag->info = transMapInfoQuery(conn, transMapInfoTbl, mappedId); +struct transMapInfo *info = transMapInfoQuery(conn, transMapInfoTbl, mappedId); -if (getSrcRec) - { char *transMapSrcTbl = trackDbRequiredSetting(tdb, transMapSrcTblSetting); - bag->src = transMapSrcQuery(conn, transMapSrcTbl, bag->info->srcDb, bag->info->srcId); - } +struct transMapSrc *src = transMapSrcQuery(conn, transMapSrcTbl, info->srcDb, info->srcId); +struct transMapGene *gene = NULL; char *transMapGeneTbl = trackDbSetting(tdb, transMapGeneTblSetting); if (transMapGeneTbl != NULL) - bag->gene = transMapGeneQuery(conn, transMapGeneTbl, - bag->info->srcDb, transMapIdToSeqId(bag->info->srcId)); -bag->srcDbIsActive = hDbIsActive(bag->info->srcDb); + gene = transMapGeneQuery(conn, transMapGeneTbl, + info->srcDb, transMapIdToSeqId(info->srcId)); +bag->srcDbIsActive = hDbIsActive(info->srcDb); +bag->meta = buildFakeBigTransMapRec(info, src, gene); +transMapInfoFree(&info); +transMapSrcFree(&src); +transMapGeneFree(&gene); +hFreeConn(&conn); +return bag; +} + +static struct transMapBag *transMapBagLoadBig(struct trackDb *tdb, char *mappedId) +/* load information from bigTransMap file */ +{ +struct sqlConnection *conn = hAllocConn(database); +struct transMapBag *bag; +AllocVar(bag); + +char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); +char *chrom = cartString(cart, "c"); +struct bbiFile *bbi = bigBedFileOpen(fileName); +struct lm *lm = lmInit(0); +int fieldIx; +struct bptFile *bpt = bigBedOpenExtraIndex(bbi, "name", &fieldIx); +struct bigBedInterval *bb = bigBedNameQuery(bbi, bpt, fieldIx, mappedId, lm); +if (slCount(bb) != 1) + errAbort("expected 1 item named \"%s\", got %d from %s", mappedId, slCount(bb), fileName); +char *fields[bbi->fieldCount]; +char startBuf[32], endBuf[32]; +int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, + bbi->fieldCount); +if (bbFieldCount != BIGTRANSMAP_NUM_COLS) + errAbort("expected %d fields in bigTransMap record, got %d in %s", + BIGTRANSMAP_NUM_COLS, bbFieldCount, fileName); +bag->psl = pslFromBigPsl(chrom, bb, 0, NULL, NULL); +bag->meta = bigTransMapLoad(fields); + +bigBedFileClose(&bbi); +lmCleanup(&lm); +hFreeConn(&conn); return bag; } static void transMapBagFree(struct transMapBag **bagPtr) /* free the bag */ { struct transMapBag *bag = *bagPtr; if (bag != NULL) { pslFree(&bag->psl); - transMapInfoFree(&bag->info); - transMapSrcFree(&bag->src); - transMapGeneFree(&bag->gene); + bigTransMapFree(&bag->meta); freez(bagPtr); } } static void prOrgScientific(char *db) /* print organism and scientific name for a database. */ { char *org = hOrganism(db); char *sciName = hScientificName(db); if ((org != NULL) && (sciName != NULL)) printf("%s (%s)", org, sciName); else printf("n/a"); freeMem(org); freeMem(sciName); } -static char *chainSubsetDesc(enum transMapInfoChainSubset cs) -/* get description for chain subset */ -{ -switch (cs) - { - case transMapInfoUnknown: - return "unknown"; - case transMapInfoAll: - return "all"; - case transMapInfoSyn: - return "syntenic"; - case transMapInfoRbest: - return "reciprocal best"; - } -return NULL; -} - static void displayMapped(struct transMapBag *bag) /* display information about the mapping alignment */ { printf("<TABLE class=\"transMap\">\n"); printf("<CAPTION>TransMap Alignment</CAPTION>\n"); printf("<TBODY>\n"); // organism/assembly printf("<TR CLASS=\"transMapLeft\"><TD>Organism<TD>"); prOrgScientific(database); printf("</TR>\n"); printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", database); // position printf("<TR CLASS=\"transMapLeft\">"); printf("<TD>Position<TD CLASS=\"transMapNoWrap\">"); printf("<A HREF=\"%s&position=%s:%d-%d\">", hgTracksPathAndSettings(), bag->psl->tName, bag->psl->tStart, bag->psl->tEnd); printf("%s:%d-%d</A>", bag->psl->tName, bag->psl->tStart, bag->psl->tEnd); printf("</TR>\n"); // % identity and % aligned printf("<TR CLASS=\"transMapLeft\"><TD>Identity<TD>%0.1f%%</TR>\n", 100.0*pslIdent(bag->psl)); printf("<TR CLASS=\"transMapLeft\"><TD>Aligned<TD>%0.1f%%</TR>\n", 100.0*pslQueryAligned(bag->psl)); -// chain used in mapping -printf("<TR CLASS=\"transMapLeft\"><TD>Chain ID<TD>%s</TR>\n", - bag->info->mappingId); +// chain type used in mapping printf("<TR CLASS=\"transMapLeft\"><TD>Chain subset<TD>%s</TR>\n", - chainSubsetDesc(bag->info->chainSubset)); + bag->meta->chainType); printf("</TBODY></TABLE>\n"); } static void displaySource(struct transMapBag *bag) /* display information about the source gene that was mapped */ { printf("<TABLE class=\"transMap\">\n"); printf("<CAPTION>Source Alignment</CAPTION>\n"); printf("<TBODY>\n"); // organism/assembly printf("<TR CLASS=\"transMapLeft\"><TD>Organism<TD>"); -prOrgScientific(bag->info->srcDb); +prOrgScientific(bag->meta->srcDb); printf("</TR>\n"); -printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", bag->info->srcDb); +printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", bag->meta->srcDb); // position printf("<TR CLASS=\"transMapLeft\"><TD>Position\n"); printf("<TD CLASS=\"transMapNoWrap\">"); if (bag->srcDbIsActive) printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\" target=_blank>" "%s:%d-%d</A>", - hgTracksName(), bag->src->db, - bag->src->chrom, bag->src->chromStart, bag->src->chromEnd, - bag->src->chrom, bag->src->chromStart, bag->src->chromEnd); + hgTracksName(), bag->meta->srcDb, + bag->meta->srcChrom, bag->meta->srcChromStart, bag->meta->srcChromEnd, + bag->meta->srcChrom, bag->meta->srcChromStart, bag->meta->srcChromEnd); else - printf("%s:%d-%d", bag->src->chrom, bag->src->chromStart, bag->src->chromEnd); + printf("%s:%d-%d", bag->meta->srcChrom, bag->meta->srcChromStart, bag->meta->srcChromEnd); printf("</TR>\n"); -// % identity and % aligned +// % identity and % aligned, values stored as 1000*fraction ident printf("<TR CLASS=\"transMapLeft\"><TD>Identity<TD>%0.1f%%</TR>\n", - 100.0*bag->src->ident); + bag->meta->srcScore/10.0); printf("<TR CLASS=\"transMapLeft\"><TD>Aligned<TD>%0.1f%%</TR>\n", - 100.0*bag->src->aligned); + bag->meta->srcAligned/10.0); // gene and CDS printf("<TR CLASS=\"transMapLeft\"><TD>Gene<TD>%s</TR>\n", - (((bag->gene != NULL) && (strlen(bag->gene->geneName) > 0)) - ? bag->gene->geneName : " ")); + strOrNbsp(bag->meta->geneName)); printf("<TR CLASS=\"transMapLeft\"><TD>Gene Id<TD>%s</TR>\n", - (((bag->gene != NULL) && (strlen(bag->gene->geneId) > 0)) - ? bag->gene->geneId : " ")); + strOrNbsp(bag->meta->geneId)); printf("<TR CLASS=\"transMapLeft\"><TD>CDS<TD>%s</TR>\n", - (((bag->gene != NULL) && (strlen(bag->gene->cds) > 0)) - ? bag->gene->cds : " ")); + strOrNbsp(bag->meta->oCDS)); printf("</TBODY></TABLE>\n"); } static void displayAligns(struct trackDb *tdb, struct transMapBag *bag) /* display cDNA alignments */ { int start = cartInt(cart, "o"); printf("<H3>mRNA/Genomic Alignments</H3>"); -printAlignmentsSimple(bag->psl, start, "hgcTransMapCdnaAli", tdb->table, bag->info->mappedId); +printAlignmentsSimple(bag->psl, start, "hgcTransMapCdnaAli", tdb->table, bag->psl->qName); } void transMapClickHandler(struct trackDb *tdb, char *mappedId) /* Handle click on a transMap tracks */ { -struct sqlConnection *conn = hAllocConn(database); -struct transMapBag *bag = transMapBagLoad(conn, tdb, mappedId, TRUE); +struct transMapBag *bag = (trackDbSetting(tdb, "bigDataUrl") == NULL) + ? transMapBagLoadDb(tdb, mappedId) + : transMapBagLoadBig(tdb, mappedId); genericHeader(tdb, mappedId); printf("<TABLE class=\"transMapLayout\">\n"); printf("<TR><TD>\n"); displayMapped(bag); printf("<TD>\n"); displaySource(bag); printf("<TD> \n"); printf("</TR>\n"); printf("<TR><TD COLSPAN=3>\n"); displayAligns(tdb, bag); printf("</TR>\n"); printf("</TABLE>\n"); printTrackHtml(tdb); transMapBagFree(&bag); -hFreeConn(&conn); } static struct dnaSeq *getCdnaSeq(struct trackDb *tdb, char *name) /* look up sequence name in seq and extFile tables specified * for base coloring. */ { /* FIXME: this is really a rip off of some of the code in * hgTracks/cds.c; really need to centralize it somewhere */ char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE); char *specCopy = cloneString(spec); // value is: extFile seqTbl extFileTbl char *words[3]; int nwords = chopByWhite(specCopy, words, ArraySize(words)); if ((nwords != ArraySize(words)) || !sameString(words[0], "extFile")) errAbort("invalid %s track setting: %s", BASE_COLOR_USE_SEQUENCE, spec); struct dnaSeq *seq = hDnaSeqMustGet(NULL, name, words[1], words[2]); freeMem(specCopy); return seq; } void transMapShowCdnaAli(struct trackDb *tdb, char *mappedId) /* Show alignment for mappedId, mostly ripped off from htcCdnaAli */ { -struct sqlConnection *conn = hAllocConn(database); -struct transMapBag *bag = transMapBagLoad(conn, tdb, mappedId, FALSE); +struct transMapBag *bag = transMapBagLoadDb(tdb, mappedId); struct genbankCds cds; -if ((bag->gene == NULL) || (strlen(bag->gene->cds) == 0) - || !genbankCdsParse(bag->gene->cds, &cds)) - ZeroVar(&cds); /* can't get or parse cds */ +if (isEmpty(bag->meta->oCDS) || !genbankCdsParse(bag->meta->oCDS, &cds)) + ZeroVar(&cds); /* can't get or parse CDS, so zero it */ struct dnaSeq *seq = getCdnaSeq(tdb, transMapIdToSeqId(mappedId)); writeFramesetType(); puts("<HTML>"); printf("<HEAD>\n<TITLE>%s vs Genomic</TITLE>\n</HEAD>\n\n", mappedId); showSomeAlignment(bag->psl, seq, gftDna, 0, seq->size, NULL, cds.start, cds.end); dnaSeqFree(&seq); transMapBagFree(&bag); -hFreeConn(&conn); }