8c8823d9a87b6046094577a808dda4ed4172b416 braney Thu Apr 23 11:09:48 2026 -0700 Make quickLifted GENCODE tracks usable: click details, position links, coloring. refs #36059 - Re-vet wgEncodeGencode* in trackHub.c:isVetted() so the quickLift hub no longer emits `avoidHandler on` for GENCODE children. Without this, hgc bypasses findNameBasedHandler and doGencodeGene is never reached, so the details page falls through to the generic showGenePos output. - In gencodeClick.c doGencodeGene/helpers, use quickLiftDb for the MySQL connection (the attrs/tag/pubMed/refSeq/uniProt tables live in the source assembly), use trackHubSkipHubName(tdb->track) for the genePred table name and the Basic/Comp/PseudoGene/PolyA prefix dispatch checks, and teach isGrcHuman/isGrcH37Native to consult the source db — otherwise the page errAborted with "BUG: gencodeClick on wrong database: hub_NNNNN_hs1". - Lift the Position values (transcript + gene bounds, 2-way pseudo, PolyA) through the quickLift chain before printing, so the details page shows destination-assembly coords and the Position link lands at a window that actually contains the gene. - htcDnaNearGene (hgc.c): when quickLifted, lift seqName/winStart/winEnd back to source coords before hgSeqItemsInRange. The prior code pointed the query at the source-assembly table but still passed the destination window, so the "Genomic Sequence from assembly" flow returned "No results returned from query." No longer reachable from the GENCODE details page (doGencodeGene writes its own Sequences table) but still hit by other quickLifted genePred tracks. - simpleTracks.c genePredItemClassColor: the hTableExists() guard was checking `database` (the destination hub db like hub_NNNNN_hs1) even though the MySQL conn was already routed to liftDb; the lookup was skipped and every item fell back to tg->ixColor, rendering all black. Check `db` instead so the gClass_* palette (coding / nonCoding / pseudo / problem) is applied. Verified end-to-end on hgwdev-braney: Gerardo's SHH test case (ENST00000297261.7) and Basic/Comp/PseudoGene/PolyA subtracks; no regression on the non-quickLifted hg38 click. diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c index bb7cdb480ac..b1bb04279ab 100644 --- src/hg/hgc/gencodeClick.c +++ src/hg/hgc/gencodeClick.c @@ -1,1036 +1,1072 @@ /* gencodeClick - click handling for GENCODE tracks */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hgc.h" +#include "trackHub.h" +#include "quickLift.h" #include "gencodeClick.h" #include "gencodeTracksCommon.h" #include "ccdsClick.h" #include "genePred.h" #include "genePredReader.h" #include "ensFace.h" #include "htmshell.h" #include "jksql.h" #include "regexHelper.h" #include "encode/wgEncodeGencodeAttrs.h" #include "encode/wgEncodeGencodeGeneSource.h" #include "encode/wgEncodeGencodePdb.h" #include "encode/wgEncodeGencodePubMed.h" #include "encode/wgEncodeGencodeRefSeq.h" #include "encode/wgEncodeGencodeTag.h" #include "encode/wgEncodeGencodeTranscriptSource.h" #include "encode/wgEncodeGencodeTranscriptSupport.h" #include "encode/wgEncodeGencodeExonSupport.h" #include "encode/wgEncodeGencodeUniProt.h" #include "encode/wgEncodeGencodeEntrezGene.h" #include "encode/wgEncodeGencodeAnnotationRemark.h" #include "encode/wgEncodeGencodeTranscriptionSupportLevel.h" #include "encode/wgEncodeGencodeGeneSymbol.h" /* * General notes: * - this will be integrated into hgGene at some point, however this was * done as part of hgc for timing reasons and to allow more time to design * the hgGene part. * - Tables below will output at least one row even if no data is available. * */ /* Various URLs and URL templates. At one time, these were in the ra file, * but that didn't prove that helpful and end up requiring updated the ra * files for every GENCODE version if a URL was added or changed. */ //FIXME: clean up RA files when CGIs no longer need them static char *ensemblTranscriptIdUrl = "http://www.ensembl.org/%s/Transcript/Summary?db=core;t=%s"; static char *ensemblGeneIdUrl = "http://www.ensembl.org/%s/Gene/Summary?db=core;t=%s"; static char *ensemblProteinIdUrl = "http://www.ensembl.org/%s/Transcript/ProteinSummary?db=core;t=%s"; static char *ensemblSupportingEvidUrl = "http://www.ensembl.org/%s/Transcript/SupportingEvidence?db=core;t=%s"; static char *ensemblH37TranscriptIdUrl = "http://grch37.ensembl.org/%s/Transcript/Summary?db=core;t=%s"; static char *ensemblH37GeneIdUrl = "http://grch37.ensembl.org/%s/Gene/Summary?db=core;t=%s"; static char *ensemblH37ProteinIdUrl = "http://grch37.ensembl.org/%s/Transcript/ProteinSummary?db=core;t=%s"; static char *ensemblH37SupportingEvidUrl = "http://grch37.ensembl.org/%s/Transcript/SupportingEvidence?db=core;t=%s"; static char *gencodeBiotypesUrl = "http://www.gencodegenes.org/pages/biotypes.html"; static char *gencodeTagsUrl = "http://www.gencodegenes.org/pages/tags.html"; static char *yalePseudoUrl = "http://tables.pseudogene.org/%s"; static char *apprisHomeUrl = "https://appris.bioinfo.cnio.es/#/"; static char *apprisGeneUrl = "https://appris.bioinfo.cnio.es/#/database/id/%s/%s?sc=ensembl"; // species-specific static char *hgncByIdUrl = "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/%s"; static char *hgncBySymUrl = " https://www.genenames.org/data/gene-symbol-report/#!/symbol/%s"; static char *geneCardsUrl = "http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s"; static char *mgiBySymUrl = "http://www.informatics.jax.org/quicksearch/summary?queryType=exactPhrase&query=%s"; static char *mgiByIdUrl = "http://www.informatics.jax.org/accession/%s"; static char* UNKNOWN = "unknown"; -static boolean isGrcHuman() -/* is this a GRC human assembly? */ +static char *gencodeSourceDb(struct trackDb *tdb) +/* return the assembly the gencode tables actually live in: the quickLiftDb + * when the track is quickLifted, otherwise the current database. */ { -//bool result = FALSE; -//if (startsWith("hg", database)) -// result = TRUE; -//else if (!startsWith("mm", database)) -// warn("BUG: gencodeClick on wrong database: %s", database); -//return result; +char *liftDb = trackDbSetting(tdb, "quickLiftDb"); +return (liftDb != NULL) ? liftDb : database; +} -if (startsWith("hg", database)) +static void liftAnnoPos(struct trackDb *tdb, char *chrom, int start, int end, + char **retChrom, int *retStart, int *retEnd) +/* If the tdb is quickLifted, translate chrom:start-end from the source + * assembly to the destination assembly the user is viewing. Otherwise + * return the input unchanged. Falls back to input on lift failure. */ +{ +*retChrom = chrom; +*retStart = start; +*retEnd = end; +char *liftDb = trackDbSetting(tdb, "quickLiftDb"); +if (liftDb != NULL) + quickLiftLiftPos(liftDb, trackHubSkipHubName(database), + chrom, start, end, retChrom, retStart, retEnd); +} + +static boolean isGrcHuman(struct trackDb *tdb) +/* is this a GRC human assembly? */ +{ +char *db = gencodeSourceDb(tdb); +if (startsWith("hg", db)) return TRUE; -else if (startsWith("mm", database)) +else if (startsWith("mm", db)) return FALSE; else - errAbort("BUG: gencodeClick on wrong database: %s", database); + errAbort("BUG: gencodeClick on wrong database: %s", db); return FALSE; } static bool haveGencodeTable(struct sqlConnection *conn, struct trackDb *tdb, char *tableBase) /* determine if a gencode table exists; it might be option or not in older releases */ { return sqlTableExists(conn, gencodeGetTableName(tdb, tableBase)); } static boolean isGrcH37Native(struct trackDb *tdb) /* Is this GENCODE GRCh37 native build, which requires a different Ensembl site. */ { // check for non-lifted GENCODE on GRCh37/hg19 -if (sameString(database, "hg19")) +if (sameString(gencodeSourceDb(tdb), "hg19")) return stringIn("lift37", gencodeGetVersion(tdb)) == NULL; else return FALSE; } static boolean isRealGeneSymbol(char* geneName, boolean haveGeneSymbolSource, struct wgEncodeGencodeGeneSymbol *geneSymbolSource) /* Attempt to determine if this is a gene symbol assigned by HGNC/MGI or a * generate one. newer versions of GENCODE have wgEncodeGencodeGeneSymbol, * which has the definitions. With older version of GENCODE guess a guess * is make by trying to match older clone-based names ones. */ { if (haveGeneSymbolSource) { return geneSymbolSource != NULL; } else { // 'A' followed by one or more letters, then followed by numbers and a '.', // followed by an incrementing gene number. static const char *regexp = "^A[A-Z]+[0-9]+\\.[0-9]+$1)"; return regexMatch(geneName, regexp); } } static int transAnnoCmp(const void *va, const void *vb) /* Compare genePreds, sorting to keep select gene first. The only cases * that annotations will be duplicated is if they are in the PAR and thus * on different chroms. */ { const struct genePred *a = *((struct genePred **)va); const struct genePred *b = *((struct genePred **)vb); if (sameString(a->name, seqName)) return -1; else if (sameString(b->name, seqName)) return 1; else return strcmp(a->name, b->name); } static bool isProteinCodingTrans(struct wgEncodeGencodeAttrs *transAttrs) /* is a transcript protein coding? */ { return sameString(transAttrs->transcriptClass, "coding"); } static struct genePred *transAnnoLoad(struct sqlConnection *conn, struct trackDb *tdb, char *gencodeId) /* load the gencode annotations and sort the one corresponding to the one that was clicked on is * first. Should only have one or two. */ { // must check chrom due to PAR char where[256]; sqlSafef(where, sizeof(where), "(chrom = \"%s\") and (name = \"%s\")", seqName, gencodeId); -struct genePred *transAnno = genePredReaderLoadQuery(conn, tdb->track, where); +struct genePred *transAnno = genePredReaderLoadQuery(conn, trackHubSkipHubName(tdb->track), where); slSort(&transAnno, transAnnoCmp); return transAnno; } static struct wgEncodeGencodeAttrs *transAttrsLoad(struct trackDb *tdb, struct sqlConnection *conn, char *gencodeId) /* load the gencode attributes */ { char query[1024]; sqlSafef(query, sizeof(query), "select * from %s where transcriptId = \"%s\"", gencodeGetTableName(tdb, "wgEncodeGencodeAttrs"), gencodeId); struct sqlResult *sr = sqlGetResult(conn, query); char **row = sqlNextRow(sr); if (row == NULL) errAbort("gencode transcript %s not found in %s", gencodeId, gencodeGetTableName(tdb, "wgEncodeGencodeAttrs")); // older version don't have proteinId column. struct wgEncodeGencodeAttrs *transAttrs = wgEncodeGencodeAttrsLoad(row, sqlCountColumns(sr)); sqlFreeResult(&sr); return transAttrs; } static void getGeneBounds(struct trackDb *tdb, struct sqlConnection *conn, struct genePred *transAnno, int *geneChromStart, int *geneChromEnd) /* find bounds for the gene */ { // must check chrom due to PAR char where[256]; sqlSafef(where, sizeof(where), "(chrom = \"%s\") and (name2 = \"%s\")", seqName, transAnno->name2); -struct genePred *geneAnnos = genePredReaderLoadQuery(conn, tdb->track, where); +struct genePred *geneAnnos = genePredReaderLoadQuery(conn, trackHubSkipHubName(tdb->track), where); struct genePred *geneAnno; *geneChromStart = transAnno->txStart; *geneChromEnd = transAnno->txEnd; for (geneAnno = geneAnnos; geneAnno != NULL; geneAnno = geneAnno->next) { *geneChromStart = min(*geneChromStart, geneAnno->txStart); *geneChromEnd = max(*geneChromEnd, geneAnno->txEnd); } genePredFreeList(&geneAnnos); } static void *metaDataLoad(struct trackDb *tdb, struct sqlConnection *conn, char *gencodeId, char *tableBase, char *keyCol, unsigned queryOpts, sqlLoadFunc loadFunc) /* load autoSql objects for gencode meta data. */ { return sqlQueryObjs(conn, loadFunc, queryOpts, "select * from %s where %s = \"%s\"", gencodeGetTableName(tdb, tableBase), keyCol, gencodeId); } static int uniProtDatasetCmp(const void *va, const void *vb) /* Compare wgEncodeGencodeUniProt by dateset */ { const struct wgEncodeGencodeUniProt *a = *((struct wgEncodeGencodeUniProt **)va); const struct wgEncodeGencodeUniProt *b = *((struct wgEncodeGencodeUniProt **)vb); return a->dataset - b->dataset; } static char *getMethodDesc(char *source) /* return the annotation method name based gene or transcript source */ { // sometimes backmap doesn't get every entry method entry mapped. Until that // is fixed, allow it to be missing // looks for being havana and/or ensembl // classifies other sources as automatic (mt_genbank_import ncrna ncrna_pseudogene) bool hasHav = containsStringNoCase(source, "havana") != NULL; bool hasEns = containsStringNoCase(source, "ensembl") != NULL; if (hasHav && hasEns) return "manual & automatic"; else if (hasHav) return "manual"; else return "automatic"; } static char *getLevelDesc(int level) /* return english description for level */ { if (level == 1) return "validated"; else if (level == 2) return "manual"; else if (level == 3) return "automatic"; else return "unknown"; } static char *getSupportLevelDesc(struct wgEncodeGencodeTranscriptionSupportLevel *tsl) /* return description for level */ { static char buf[32]; if ((tsl == NULL) || (tsl->level <= 0)) return "tslNA"; else { safef(buf, sizeof(buf), "tsl%d", tsl->level); return buf; } } static char* getScientificNameSym(void) /* get the scientific name of an organism in the form "Homo_sapiens" * WARNING: static return */ { static char sciNameSym[128]; char *sciName = hScientificName(database); if (sciName == NULL) errAbort("can't get scientific name for %s", database); safecpy(sciNameSym, sizeof(sciNameSym), sciName); freeMem(sciName); subChar(sciNameSym, ' ', '_'); return sciNameSym; } static void prExtIdAnchor(char *id, char *urlTemplate) /* if an id to an external database is not empty, print an HTML anchor to it */ { if (!isEmpty(id)) { char urlBuf[512]; safef(urlBuf, sizeof(urlBuf), urlTemplate, id); printf("<a href=\"%s\" target=_blank>%s</a>", urlBuf, id); } } #if UNUSED static void prTdExtIdAnchor(char *id, char *urlTemplate) /* print a table data element with an anchor for a id */ { printf("<td>"); prExtIdAnchor(id, urlTemplate); } #endif static void prEnsIdAnchor(char *id, char *urlTemplate) /* if an id to an ensembl database is not empty, print an HTML anchor to it */ { if (!isEmpty(id)) { char idBuf[64], urlBuf[512]; /* The lift37 releases append a '_N' modifier to the ids to indicate the are * mapped. N is an integer mapping version. Don't include this in link if it exists. */ safecpy(idBuf, sizeof(idBuf), id); char *p = strchr(idBuf, '_'); if (p != NULL) *p = '\0'; safef(urlBuf, sizeof(urlBuf), urlTemplate, getScientificNameSym(), idBuf); printf("<a href=\"%s\" target=_blank>%s</a>", urlBuf, id); } } static void prTdEnsIdAnchor(char *id, char *urlTemplate) /* print a table data element with an ensembl anchor for a id */ { printf("<td>"); prEnsIdAnchor(id, urlTemplate); } static void prApprisTdAnchor(char *id, char *label, char *urlTemplate) /* print a gene or transcript link to APPRIS */ { // under bar separated, lower case species name. char *speciesArg = hScientificName(database); toLowerN(speciesArg, strlen(speciesArg)); subChar(speciesArg, ' ', '_'); char accBuf[64]; printf("<td><a href=\""); printf(urlTemplate, speciesArg, gencodeBaseAcc(id, accBuf, sizeof(accBuf))); printf("\" target=_blank>%s</a>", label); freeMem(speciesArg); } static void writePosLink(char *chrom, int chromStart, int chromEnd) /* write link to a genomic position */ { printf("<a href=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>", hgTracksPathAndSettings(), database, chrom, chromStart, chromEnd, chrom, chromStart+1, chromEnd); } static bool geneHasApprisTranscripts(struct trackDb *tdb, struct sqlConnection *conn, struct wgEncodeGencodeAttrs *transAttrs) /* check if any transcript in a gene has an APPRIS tags */ { char query[1024]; sqlSafef(query, sizeof(query), "%s tag where tag.tag like 'appris%%' and transcriptId in " "(select transcriptId from %s where geneId='%s')", gencodeGetTableName(tdb, "wgEncodeGencodeTag"), gencodeGetTableName(tdb, "wgEncodeGencodeAttrs"), transAttrs->geneId); return sqlRowCount(conn, query) > 0; } static char* findApprisTag(struct wgEncodeGencodeTag *tags) /* search list for APPRIS tag or NULL */ { struct wgEncodeGencodeTag *tag; for (tag = tags; tag != NULL; tag = tag->next) { if (startsWith("appris_", tag->tag)) return tag->tag; } return NULL; } static char* apprisTagToSymbol(char* tag) /* convert APPRIS tag to the symbol use by APPRIS. WARNING static return. */ { // appris_principal_1 -> PRINCIPAL:1 static char buf[64]; safecpy(buf, sizeof(buf), tag+7); touppers(buf); subChar(buf, '_', ':'); return buf; } static void writeAprrisRow(struct sqlConnection *conn, struct trackDb *tdb, struct wgEncodeGencodeAttrs *transAttrs, struct wgEncodeGencodeTag *tags) /* write row for APPRIS */ { // Get labels to use. if transcript has an appris tag, then we link to the transcript. // if it doesn;t have a appris tag, we can still link to the gene if any of the transcripts // have appris tags char* apprisTag = findApprisTag(tags); char* transLabel = (apprisTag != NULL) ? apprisTagToSymbol(apprisTag) : NULL; char *geneLabel = ((apprisTag != NULL) || geneHasApprisTranscripts(tdb, conn, transAttrs)) ? transAttrs->geneName : NULL; // APPRIS gene and transcript now go to the same location printf("<tr><th><a href=\"%s\" target=_blank>APPRIS</a>\n", apprisHomeUrl); if (transLabel != NULL) prApprisTdAnchor(transAttrs->geneId, transLabel, apprisGeneUrl); else printf("<td> "); if (geneLabel != NULL) prApprisTdAnchor(transAttrs->geneId, geneLabel, apprisGeneUrl); else printf("<td> "); printf("</tr>\n"); } static void writeHumanGeneLinkout(struct wgEncodeGencodeAttrs *transAttrs, boolean haveGeneSymbolSource, struct wgEncodeGencodeGeneSymbol *geneSymbolSource) /* Write external gene database links for human if they appear to be a real * gene symbol Getting it wrong is not a disaster, as the target database will * just report not found. */ { boolean isReal = isRealGeneSymbol(transAttrs->geneName, haveGeneSymbolSource, geneSymbolSource); printf("<tr><th>HGNC gene information<td colspan=2>"); if (isReal) { if (haveGeneSymbolSource) prExtIdAnchor(geneSymbolSource->geneId, hgncByIdUrl); else prExtIdAnchor(transAttrs->geneName, hgncBySymUrl); } printf("</tr>\n"); printf("<tr><th>GeneCards<td colspan=2>"); if (isReal) prExtIdAnchor(transAttrs->geneName, geneCardsUrl); printf("</tr>\n"); } static void writeMouseGeneLinkout(struct wgEncodeGencodeAttrs *transAttrs, boolean haveGeneSymbolSource, struct wgEncodeGencodeGeneSymbol *geneSymbolSource) /* Write external gene database links for mouse if they appear to be a real * gene symbol Getting it wrong is not a disaster, as the target database will * just report not found. */ { boolean isReal = isRealGeneSymbol(transAttrs->geneName, haveGeneSymbolSource, geneSymbolSource); printf("<tr><th>MGI gene information<td colspan=2>"); if (isReal) { if (haveGeneSymbolSource) prExtIdAnchor(geneSymbolSource->geneId, mgiByIdUrl); else prExtIdAnchor(transAttrs->geneName, mgiBySymUrl); } printf("</tr>\n"); } static void writeBasicInfoHtml(struct sqlConnection *conn, struct trackDb *tdb, char *gencodeId, struct genePred *transAnno, struct wgEncodeGencodeAttrs *transAttrs, int geneChromStart, int geneChromEnd, struct wgEncodeGencodeGeneSource *geneSource, struct wgEncodeGencodeTranscriptSource *transcriptSource, struct wgEncodeGencodeTag *tags, bool haveTsl, struct wgEncodeGencodeTranscriptionSupportLevel *tsl, boolean haveGeneSymbolSource, struct wgEncodeGencodeGeneSymbol *geneSymbolSource) /* write basic HTML info for all genes */ { // basic gene and transcript information printf("<table class=\"hgcCcds\" style=\"white-space: nowrap;\"><thead>\n"); printf("<tr><th><th>Transcript<th>Gene</tr>\n"); printf("</thead><tbody>\n"); printf("<tr><th>GENCODE id"); prTdEnsIdAnchor(transAttrs->transcriptId, (isGrcH37Native(tdb) ? ensemblH37TranscriptIdUrl: ensemblTranscriptIdUrl)); prTdEnsIdAnchor(transAttrs->geneId, (isGrcH37Native(tdb) ? ensemblH37GeneIdUrl : ensemblGeneIdUrl)); printf("</tr>\n"); printf("<tr><th>Name"); printf("<td>%s", transAttrs->transcriptName); printf("<td>%s", transAttrs->geneName); printf("</tr>\n"); if (isNotEmpty(transAttrs->proteinId)) { // protein id in database, maybe not for this transcript printf("<tr><th>Protein id"); if (strlen(transAttrs->proteinId) > 0) prTdEnsIdAnchor(transAttrs->proteinId, (isGrcH37Native(tdb) ? ensemblH37ProteinIdUrl: ensemblProteinIdUrl)); else printf("<td> "); printf("<td>"); printf("</tr>\n"); } printf("<tr><th>HAVANA manual id"); printf("<td>%s", transAttrs->havanaTranscriptId); printf("<td>%s", transAttrs->havanaGeneId); printf("</tr>\n"); +char *transChrom, *geneChrom; +int transStart, transEnd, gStart, gEnd; +liftAnnoPos(tdb, transAnno->chrom, transAnno->txStart, transAnno->txEnd, + &transChrom, &transStart, &transEnd); +liftAnnoPos(tdb, transAnno->chrom, geneChromStart, geneChromEnd, + &geneChrom, &gStart, &gEnd); printf("<tr><th>Position"); printf("<td>"); -writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd); +writePosLink(transChrom, transStart, transEnd); printf("<td>"); -writePosLink(transAnno->chrom, geneChromStart, geneChromEnd); +writePosLink(geneChrom, gStart, gEnd); printf("</tr>\n"); printf("<tr><th>Strand<td>%s<td></tr>\n", transAnno->strand); printf("<tr><th><a href=\"%s\" target = _blank>Biotype</a><td>%s<td>%s</tr>\n", gencodeBiotypesUrl, transAttrs->transcriptType, transAttrs->geneType); printf("<tr><th>Annotation Level<td>%s (%d)<td></tr>\n", getLevelDesc(transAttrs->level), transAttrs->level); char *transSrcDesc = (transcriptSource != NULL) ? getMethodDesc(transcriptSource->source) : UNKNOWN; char *geneSrcDesc = (geneSource != NULL) ? getMethodDesc(geneSource->source) : UNKNOWN; printf("<tr><th>Annotation Method<td>%s<td>%s</tr>\n", transSrcDesc, geneSrcDesc); if (haveTsl) { char *tslDesc = getSupportLevelDesc(tsl); printf("<tr><th><a href=\"#tsl\">Transcription Support Level</a><td><a href=\"#%s\">%s</a><td></tr>\n", tslDesc, tslDesc); } -if (isGrcHuman()) +if (isGrcHuman(tdb)) writeHumanGeneLinkout(transAttrs, haveGeneSymbolSource, geneSymbolSource); else writeMouseGeneLinkout(transAttrs, haveGeneSymbolSource, geneSymbolSource); printf("<tr><th>CCDS<td>"); if (!isEmpty(transAttrs->ccdsId)) { printf("<a href=\""); printCcdsExtUrl(transAttrs->ccdsId); printf("\" target=_blank>%s</a>", transAttrs->ccdsId); } printf("<td></tr>\n"); if (transAttrs->transcriptRank > 0) { // older versions will have rank of zero printf("<tr><th>Transcript rank<td>%d<td></tr>\n", transAttrs->transcriptRank); } if (isProteinCodingTrans(transAttrs)) writeAprrisRow(conn, tdb, transAttrs, tags); // FIXME: add sequence here?? printf("</tbody></table>\n"); } static void writeSequenceHtml(struct trackDb *tdb, char *gencodeId, struct genePred *transAnno) /* write links to get sequences */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"2\">Sequences</tr>\n"); printf("</thead><tbody>\n"); if (transAnno->cdsStart < transAnno->cdsEnd) { // protein coding printf("<tr><td width=\"50%%\">"); hgcAnchorSomewhere("htcGeneMrna", gencodeId, tdb->table, seqName); printf("Predicted mRNA</a>"); printf("<td width=\"50%%\">"); hgcAnchorSomewhere("htcTranslatedPredMRna", gencodeId, "translate", seqName); printf("Predicted protein</a></tr>\n"); } else { // non-protein coding printf("<tr><td width=\"50%%\">"); hgcAnchorSomewhere("htcGeneMrna", gencodeId, tdb->table, seqName); printf("Predicted mRNA</a><td width=\"50%%\"></tr>\n"); } printf("</tbody></table>\n"); } static void writeAnnotationRemarkHtml(struct wgEncodeGencodeAnnotationRemark *remarks) /* write HTML links to remarks */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"1\">Annotation Remarks</tr>\n"); printf("</thead><tbody>\n"); // make sure at least one empty row in printed if (remarks == NULL) printf("<tr><td></td></tr>\n"); struct wgEncodeGencodeAnnotationRemark *remark; for (remark = remarks; remark != NULL; remark = remark->next) { char *encRemark = htmlEncode(remark->remark); printf("<tr><td>%s</td></tr>\n", encRemark); freeMem(encRemark); } printf("</tbody></table>\n"); } static void writePdbLinkHtml(struct wgEncodeGencodePdb *pdbs) /* write HTML links to PDB */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"3\">Protein Data Bank</tr>\n"); printf("</thead><tbody>\n"); struct wgEncodeGencodePdb *pdb = pdbs; int i, rowCnt = 0; while ((pdb != NULL) || (rowCnt == 0)) { printf("<tr>"); for (i = 0; i < 3; i++) { printf("<td width=\"33.33%%\">"); if (pdb != NULL) { printf("<a href=\"https://www.rcsb.org/structure/%s\" target=_blank>%s</a>", pdb->pdbId, pdb->pdbId); pdb = pdb->next; } } printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); } static void writePubMedEntry(struct wgEncodeGencodePubMed *pubMed) /* write HTML table entry for a pubMed */ { printf("<td width=\"33.33%%\"><a href=\""); printEntrezPubMedUidUrl(stdout, pubMed->pubMedId); printf("\" target=_blank>%d</a>", pubMed->pubMedId); } static void writePubMedLinkHtml(struct wgEncodeGencodePubMed *pubMeds) /* write HTML links to PubMed */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"3\">PubMed</tr>\n"); printf("</thead><tbody>\n"); struct wgEncodeGencodePubMed *pubMed = pubMeds; int i, rowCnt = 0; while ((pubMed != NULL) || (rowCnt == 0)) { printf("<tr>"); for (i = 0; i < 3; i++) { if (pubMed != NULL) { writePubMedEntry(pubMed); pubMed = pubMed->next; } else printf("<td width=\"33.33%%\">"); } printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); } static void writeEntrezGeneEntry(struct wgEncodeGencodeEntrezGene *entrezGene) /* write HTML table entry for a entrezGene */ { printf("<td width=\"33.33%%\"><a href=\""); printEntrezGeneUrl(stdout, entrezGene->entrezGeneId); printf("\" target=_blank>%d</a>", entrezGene->entrezGeneId); } static void writeEntrezGeneLinkHtml(struct wgEncodeGencodeEntrezGene *entrezGenes) /* write HTML links to EntrezGene */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"3\">Entrez Gene</tr>\n"); printf("</thead><tbody>\n"); struct wgEncodeGencodeEntrezGene *entrezGene = entrezGenes; int i, rowCnt = 0; while ((entrezGene != NULL) || (rowCnt == 0)) { printf("<tr>"); for (i = 0; i < 3; i++) { if (entrezGene != NULL) { writeEntrezGeneEntry(entrezGene); entrezGene = entrezGene->next; } else printf("<td width=\"33.33%%\">"); } printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); } static void writeRefSeqEntry(struct wgEncodeGencodeRefSeq *refSeq) /* write HTML table entry for a RefSeq */ { printf("<td width=\"50%%\"><a href=\""); printEntrezNucleotideUrl(stdout, refSeq->rnaAcc); printf("\" target=_blank>%s</a>", refSeq->rnaAcc); printf("<td width=\"50%%\">"); if (!isEmpty(refSeq->pepAcc)) { printf("<a href=\""); printEntrezProteinUrl(stdout, refSeq->pepAcc); printf("\" target=_blank>%s</a>", refSeq->pepAcc); } } static void writeRefSeqLinkHtml(struct wgEncodeGencodeRefSeq *refSeqs) /* write HTML links to RefSeq */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"2\">RefSeq</tr>\n"); printf("<tr class=\"hgcCcdsSub\"><th>RNA<th>Protein</tr>\n"); printf("</thead><tbody>\n"); struct wgEncodeGencodeRefSeq *refSeq = refSeqs; int rowCnt = 0; while ((refSeq != NULL) || (rowCnt == 0)) { printf("<tr>"); if (refSeq != NULL) { writeRefSeqEntry(refSeq); refSeq = refSeq->next; } else printf("<td width=\"50%%\"><td width=\"50%%\">"); printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); } static void writeUniProtEntry(struct wgEncodeGencodeUniProt *uniProt) /* write HTML table entry for a UniProt */ { printf("<td width=\"15%%\">%s", (uniProt->dataset == wgEncodeGencodeUniProtSwissProt) ? "SwissProt" : "TrEMBL"); printf("<td width=\"15%%\"><a href=\""); printSwissProtAccUrl(stdout, uniProt->acc); printf("\" target=_blank>%s</a>", uniProt->acc); printf("<td width=\"20%%\"><a href=\""); printSwissProtAccUrl(stdout, uniProt->name); printf("\" target=_blank>%s</a>", uniProt->name); } static void writeUniProtLinkHtml(struct wgEncodeGencodeUniProt *uniProts) /* write HTML links to UniProt */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"6\">UniProt</tr>\n"); printf("<tr class=\"hgcCcdsSub\"><th>Data set<th>Accession<th>Name<th>Data set<th>Accession<th>Name</tr>\n"); printf("</thead><tbody>\n"); int i, rowCnt = 0; struct wgEncodeGencodeUniProt *uniProt = uniProts; while ((uniProt != NULL) || (rowCnt == 0)) { printf("<tr>"); for (i = 0; i < 2; i++) { if (uniProt != NULL) { writeUniProtEntry(uniProt); uniProt = uniProt->next; } else printf("<td width=\"50%%\" colspan=3>"); } printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); } struct supportEvid /* temporary struct for subset of supporting information displayed */ { struct supportEvid *next; char *seqId; /* sequence id (memory not owned) */ char *seqSrc; /* evidence source database (memory not owned) */ }; static int supportEvidCmp(const void *va, const void *vb) /* Compare two supportEvid objects. */ { const struct supportEvid *a = *((struct supportEvid **)va); const struct supportEvid *b = *((struct supportEvid **)vb); int diff = strcmp(a->seqSrc, b->seqSrc); if (diff == 0) diff = strcmp(a->seqId, b->seqId); return diff; } static void transcriptSupportToSupportEvid(struct supportEvid **supportEvids, struct wgEncodeGencodeTranscriptSupport *transcriptSupports) /* convert transcriptSupport to common structure */ { struct wgEncodeGencodeTranscriptSupport *transcriptSupport; for (transcriptSupport = transcriptSupports; transcriptSupport != NULL; transcriptSupport = transcriptSupport->next) { struct supportEvid *supportEvid; AllocVar(supportEvid); supportEvid->seqId = transcriptSupport->seqId; supportEvid->seqSrc = transcriptSupport->seqSrc; slAddHead(supportEvids, supportEvid); } } static void exonSupportToSupportEvid(struct supportEvid **supportEvids, struct wgEncodeGencodeExonSupport *exonSupports) /* convert exonSupport to common structure */ { struct wgEncodeGencodeExonSupport *exonSupport; for (exonSupport = exonSupports; exonSupport != NULL; exonSupport = exonSupport->next) { struct supportEvid *supportEvid; AllocVar(supportEvid); supportEvid->seqId = exonSupport->seqId; supportEvid->seqSrc = exonSupport->seqSrc; slAddHead(supportEvids, supportEvid); } } static void sortUniqSupportExidence(struct supportEvid **supportEvids) /* sort support evidence and make unique */ { struct supportEvid *supportEvid, *supportEvids2 = NULL; slSort(supportEvids, supportEvidCmp); // make unique while ((supportEvid = slPopHead(supportEvids)) != NULL) { if ((supportEvids2 == NULL) || (supportEvidCmp(&supportEvid, &supportEvids2) != 0)) slAddHead(&supportEvids2, supportEvid); else freeMem(supportEvid); } slReverse(&supportEvids2); *supportEvids = supportEvids2; } static struct supportEvid *loadSupportEvid(struct wgEncodeGencodeTranscriptSupport *transcriptSupports, struct wgEncodeGencodeExonSupport *exonSupports) /* load transcript and supporting evidence into a common structure */ { struct supportEvid *supportEvids = NULL; transcriptSupportToSupportEvid(&supportEvids, transcriptSupports); exonSupportToSupportEvid(&supportEvids, exonSupports); sortUniqSupportExidence(&supportEvids); return supportEvids; } static void writeSupportEvidenceEntry(struct supportEvid *supportEvid) /* write HTML table entry for a supporting evidence */ { // FIXME: should link to sources when possible printf("<td width=\"25%%\">%s", supportEvid->seqSrc); printf("<td width=\"25%%\">%s", supportEvid->seqId); } static void writeSupportingEvidenceLinkHtml(struct trackDb *tdb, char *gencodeId, struct wgEncodeGencodeTranscriptSupport *transcriptSupports, struct wgEncodeGencodeExonSupport *exonSupports) /* write HTML links to supporting evidence */ { struct supportEvid *supportEvids = loadSupportEvid(transcriptSupports, exonSupports); printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=\"4\">Supporting Evidence ("); prEnsIdAnchor(gencodeId, (isGrcH37Native(tdb) ? ensemblH37SupportingEvidUrl: ensemblSupportingEvidUrl)); printf(")</tr>\n"); printf("<tr class=\"hgcCcdsSub\"><th>Source<th>Sequence<th>Source<th>Sequence</tr>\n"); printf("</thead><tbody>\n"); struct supportEvid *supportEvid = supportEvids; int i, rowCnt = 0; while ((supportEvid != NULL) || (rowCnt == 0)) { printf("<tr>"); for (i = 0; i < 2; i++) { if (supportEvid != NULL) { writeSupportEvidenceEntry(supportEvid); supportEvid = supportEvid->next; } else printf("<td colspan=\"2\" width=\"50%%\">"); } printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); slFreeList(&supportEvids); } static void writeTagEntry(struct wgEncodeGencodeTag *tag) /* write HTML table entry for a Tag */ { // FIXME: link to help once gencodegenes.org has it printf("<td width=\"33.33%%\">%s", tag->tag); } static void writeTagLinkHtml(struct wgEncodeGencodeTag *tags) /* write HTML links to Tag */ { printf("<table class=\"hgcCcds\"><thead>\n"); printf("<tr><th colspan=3><a href=\"%s\" target=_blank>Tags</a></tr>\n", gencodeTagsUrl); printf("</thead><tbody>\n"); int i, rowCnt = 0; struct wgEncodeGencodeTag *tag = tags; while ((tag != NULL) || (rowCnt == 0)) { printf("<tr>"); for (i = 0; i < 3; i++) { if (tag != NULL) { writeTagEntry(tag); tag = tag->next; } else printf("<td width=\"33.33%%\">"); } printf("</tr>\n"); rowCnt++; } printf("</tbody></table>\n"); } static void doGencodeGeneTrack(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *transAnno) /* Process click on a GENCODE gene annotation track. */ { struct wgEncodeGencodeAttrs *transAttrs = transAttrsLoad(tdb, conn, gencodeId); char *gencodeGeneId = transAttrs->geneId; struct wgEncodeGencodeGeneSource *geneSource = metaDataLoad(tdb, conn, gencodeGeneId, "wgEncodeGencodeGeneSource", "geneId", sqlQuerySingle, (sqlLoadFunc)wgEncodeGencodeGeneSourceLoad); struct wgEncodeGencodeTranscriptSource *transcriptSource = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptSource", "transcriptId", sqlQuerySingle, (sqlLoadFunc)wgEncodeGencodeTranscriptSourceLoad); bool haveRemarks = haveGencodeTable(conn, tdb, "wgEncodeGencodeAnnotationRemark"); struct wgEncodeGencodeAnnotationRemark *remarks = haveRemarks ? metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeAnnotationRemark", "transcriptId", 0, (sqlLoadFunc)wgEncodeGencodeAnnotationRemarkLoad) : NULL; struct wgEncodeGencodePdb *pdbs = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodePdb", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodePdbLoad); struct wgEncodeGencodePubMed *pubMeds = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodePubMed", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodePubMedLoad); bool haveEntrezGene = haveGencodeTable(conn, tdb, "wgEncodeGencodeEntrezGene"); struct wgEncodeGencodeEntrezGene *entrezGenes = haveEntrezGene ? metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeEntrezGene", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeEntrezGeneLoad) : NULL; struct wgEncodeGencodeRefSeq *refSeqs = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeRefSeq", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeRefSeqLoad); struct wgEncodeGencodeTag *tags = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTag", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeTagLoad); struct wgEncodeGencodeTranscriptSupport *transcriptSupports = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptSupport", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeTranscriptSupportLoad); struct wgEncodeGencodeExonSupport *exonSupports = NULL; // exonSupports not available in back mapped GENCODE releases if (haveGencodeTable(conn, tdb, "wgEncodeGencodeExonSupport")) exonSupports = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeExonSupport", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeExonSupportLoad); struct wgEncodeGencodeUniProt *uniProts = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeUniProt", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeUniProtLoad); slSort(&uniProts, uniProtDatasetCmp); bool haveTsl = haveGencodeTable(conn, tdb, "wgEncodeGencodeTranscriptionSupportLevel"); struct wgEncodeGencodeTranscriptionSupportLevel *tsl = haveTsl ? metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptionSupportLevel", "transcriptId", 0, (sqlLoadFunc)wgEncodeGencodeTranscriptionSupportLevelLoad) : NULL; boolean haveGeneSymbolSource = haveGencodeTable(conn, tdb, "wgEncodeGencodeGeneSymbol"); struct wgEncodeGencodeGeneSymbol *geneSymbolSource = haveGeneSymbolSource ? metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeGeneSymbol", "transcriptId", 0, (sqlLoadFunc)wgEncodeGencodeGeneSymbolLoad) : NULL; int geneChromStart, geneChromEnd; getGeneBounds(tdb, conn, transAnno, &geneChromStart, &geneChromEnd); char title[256]; safef(title, sizeof(title), "GENCODE V%s Transcript Annotation", gencodeGetVersion(tdb)); char header[256]; safef(header, sizeof(header), "%s %s", title, gencodeId); if (!isEmpty(transAttrs->geneName)) safef(header, sizeof(header), "%s %s (%s)", title, gencodeId, transAttrs->geneName); else safef(header, sizeof(header), "%s %s", title, gencodeId); cartWebStart(cart, database, "%s", header); printf("<H2>%s</H2>\n", header); writeBasicInfoHtml(conn, tdb, gencodeId, transAnno, transAttrs, geneChromStart, geneChromEnd, geneSource, transcriptSource, tags, haveTsl, tsl, haveGeneSymbolSource, geneSymbolSource); writeTagLinkHtml(tags); writeSequenceHtml(tdb, gencodeId, transAnno); if (haveRemarks) writeAnnotationRemarkHtml(remarks); if (isProteinCodingTrans(transAttrs)) writePdbLinkHtml(pdbs); writePubMedLinkHtml(pubMeds); if (haveEntrezGene) writeEntrezGeneLinkHtml(entrezGenes); writeRefSeqLinkHtml(refSeqs); if (isProteinCodingTrans(transAttrs)) writeUniProtLinkHtml(uniProts); writeSupportingEvidenceLinkHtml(tdb, gencodeId, transcriptSupports, exonSupports); wgEncodeGencodeAttrsFree(&transAttrs); wgEncodeGencodeAnnotationRemarkFreeList(&remarks); wgEncodeGencodeGeneSourceFreeList(&geneSource); wgEncodeGencodeTranscriptSourceFreeList(&transcriptSource); wgEncodeGencodePdbFreeList(&pdbs); wgEncodeGencodePubMedFreeList(&pubMeds); wgEncodeGencodeEntrezGeneFreeList(&entrezGenes); wgEncodeGencodeRefSeqFreeList(&refSeqs); wgEncodeGencodeTranscriptSupportFreeList(&transcriptSupports); wgEncodeGencodeExonSupportFreeList(&exonSupports); wgEncodeGencodeUniProtFreeList(&uniProts); wgEncodeGencodeGeneSymbolFreeList(&geneSymbolSource); wgEncodeGencodeTranscriptionSupportLevelFreeList(&tsl); } static void doGencodeGene2WayPseudo(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *pseudoAnno) /* Process click on a GENCODE two-way pseudogene annotation track. */ { char header[256]; safef(header, sizeof(header), "GENCODE 2-way consensus pseudogene %s", gencodeId); cartWebStart(cart, database, "%s", header); printf("<H2>%s</H2>\n", header); printf("<b>Yale id:</b> "); prExtIdAnchor(gencodeId, yalePseudoUrl); printf("<br>"); -printPos(pseudoAnno->chrom, pseudoAnno->txStart, pseudoAnno->txEnd, pseudoAnno->strand, FALSE, NULL); +char *chrom; +int start, end; +liftAnnoPos(tdb, pseudoAnno->chrom, pseudoAnno->txStart, pseudoAnno->txEnd, &chrom, &start, &end); +printPos(chrom, start, end, pseudoAnno->strand, FALSE, NULL); } static void doGencodeGenePolyA(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *polyAAnno) /* Process click on a GENCODE poly-A annotation track. */ { char header[256]; safef(header, sizeof(header), "GENCODE PolyA Annotation %s (%s)", polyAAnno->name2, gencodeId); cartWebStart(cart, database, "%s", header); printf("<H2>%s</H2>\n", header); printf("<b>Annotation id:</b> %s<br>", gencodeId); printf("<b>Annotation Type:</b> %s<br>",polyAAnno->name2); -printPos(polyAAnno->chrom, polyAAnno->txStart, polyAAnno->txEnd, polyAAnno->strand, FALSE, NULL); +char *chrom; +int start, end; +liftAnnoPos(tdb, polyAAnno->chrom, polyAAnno->txStart, polyAAnno->txEnd, &chrom, &start, &end); +printPos(chrom, start, end, polyAAnno->strand, FALSE, NULL); } void doGencodeGene(struct trackDb *tdb, char *gencodeId) /* Process click on a GENCODE annotation. */ { -struct sqlConnection *conn = hAllocConn(database); +// When the track is quickLifted, all GENCODE metadata tables live in the +// source assembly (quickLiftDb), not in the currently-displayed destination. +char *liftDb = trackDbSetting(tdb, "quickLiftDb"); +char *metaDb = (liftDb != NULL) ? liftDb : database; +struct sqlConnection *conn = hAllocConn(metaDb); struct genePred *anno = transAnnoLoad(conn, tdb, gencodeId); -if (startsWith("wgEncodeGencodeBasic", tdb->track) - || startsWith("wgEncodeGencodeComp", tdb->track) - || startsWith("wgEncodeGencodePseudoGene", tdb->track)) +char *track = trackHubSkipHubName(tdb->track); +if (startsWith("wgEncodeGencodeBasic", track) + || startsWith("wgEncodeGencodeComp", track) + || startsWith("wgEncodeGencodePseudoGene", track)) doGencodeGeneTrack(tdb, gencodeId, conn, anno); -else if (startsWith("wgEncodeGencode2wayConsPseudo", tdb->track)) +else if (startsWith("wgEncodeGencode2wayConsPseudo", track)) doGencodeGene2WayPseudo(tdb, gencodeId, conn, anno); -else if (startsWith("wgEncodeGencodePolya", tdb->track)) +else if (startsWith("wgEncodeGencodePolya", track)) doGencodeGenePolyA(tdb, gencodeId, conn, anno); else errAbort("doGencodeGene: track not handled: \"%s\"", tdb->track); htmlHorizontalLine(); printTrackHtml(tdb); genePredFreeList(&anno); hFreeConn(&conn); } bool isNewGencodeGene(struct trackDb *tdb) /* is this a new-style gencode (>= V7) track, as indicated by * the presence of the wgEncodeGencodeVersion setting */ { return trackDbSetting(tdb, "wgEncodeGencodeVersion") != NULL; }