7976e2588e92dca0567231cf3998759bf6f1827f max Thu May 7 03:27:42 2015 -0700 implementing the external tools "send to" menu, refs #15113 diff --git src/hg/hgc/lrgClick.c src/hg/hgc/lrgClick.c index 1199348..23fed27 100644 --- src/hg/hgc/lrgClick.c +++ src/hg/hgc/lrgClick.c @@ -1,251 +1,256 @@ /* lrgClick.c - Locus Reference Genomic (LRG) sequences mapped to genome assembly */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hgc.h" #include "bigBed.h" #include "fa.h" #include "genbank.h" #include "hdb.h" #include "trackHub.h" #include "lrg.h" +#include "hui.h" INLINE void printStartAndMaybeEnd(uint start, uint end) { if (end == start+1) printf("%d", end); else printf("%d-%d", start+1, end); } static void printLrgDiffs(struct lrg *lrg, struct lrgDiff *diffList) /* Diffstr is a comma-separated list of colon-separated blkStart, lrgStart, assemblySeq, lrgSeq. * Make it more readable as a table with links to position ranges. */ { printf("\n" "" ""); struct lrgDiff *diff; for (diff = diffList; diff != NULL; diff = diff->next) { printf("\n", diff->chromSeq); } printf("
%s
location		%s
sequence		%s
location		%s
sequence", lrg->name, lrg->name, database, database); if (lrg->strand[0] == '-') printf("
(on - strand)"); printf("
"); printStartAndMaybeEnd(diff->lrgStart, diff->lrgEnd); printf("%s", diff->lrgSeq); // Make position links that are zoomed out a tiny bit from the actual positions: const int rangeFudge = 10; uint rangeStart = (diff->chromStart <= rangeFudge) ? 0 : diff->chromStart - rangeFudge; uint rangeEnd = diff->chromEnd + rangeFudge; printf("%s:", hgTracksPathAndSettings(), database, lrg->chrom, rangeStart+1, rangeEnd, lrg->chrom); printStartAndMaybeEnd(diff->chromStart, diff->chromEnd); printf("%s
\n"); slNameFreeList(&diffList); } void doLrg(struct trackDb *tdb, char *item) /* Locus Reference Genomic (LRG) track info. */ { char *chrom = cartString(cart, "c"); int start = cgiInt("o"); int end = cgiInt("t"); struct sqlConnection *conn = NULL ; if (!trackHubDatabase(database)) conn = hAllocConnTrack(database, tdb); char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); hFreeConn(&conn); if (isEmpty(fileName)) { errAbort("doLrg: missing bigBed fileName for track '%s'", tdb->track); } genericHeader(tdb, item); // Get column urls from trackDb: char *urlsStr = trackDbSetting(tdb, "urls"); struct hash *columnUrls = hashFromString(urlsStr); // Open BigWig file and get interval list. struct bbiFile *bbi = bigBedFileOpen(fileName); int bedSize = bbi->definedFieldCount; int fieldCount = bbi->fieldCount; struct lm *lm = lmInit(0); struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); boolean found = FALSE; struct bigBedInterval *bb; for (bb = bbList; bb != NULL; bb = bb->next) { if (!(bb->start == start && bb->end == end)) continue; char *fields[fieldCount]; char startBuf[16], endBuf[16]; int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, fieldCount); if (bbFieldCount != fieldCount) errAbort("doLrg: inconsistent fieldCount (bbi has %d, row has %d)", fieldCount, bbFieldCount); struct lrg *lrg = lrgLoad(fields); if (differentString(lrg->name, item)) continue; found = TRUE; printCustomUrl(tdb, lrg->name, TRUE); bedPrintPos((struct bed *)lrg, bedSize, tdb); char *url = hashFindVal(columnUrls, "hgncId"); printf("HGNC Gene Symbol: "); if (isNotEmpty(url)) { char hgncIdStr[32]; safef(hgncIdStr, sizeof(hgncIdStr), "%d", lrg->hgncId); - char *idUrl = replaceInUrl(tdb, url, hgncIdStr, TRUE); + char *idUrl = replaceInUrl(url, hgncIdStr, cart, database, seqName, winStart, + winEnd, tdb->track, TRUE); printf("%s
\n", idUrl, lrg->hgncSymbol); } else printf("%s
\n", lrg->hgncSymbol); printf("Source of LRG sequence: " "%s
\n", lrg->lrgSourceUrl, lrg->lrgSource); printf("LRG Sequence at NCBI: "); url = hashFindVal(columnUrls, "ncbiAcc"); if (isNotEmpty(url)) { - char *idUrl = replaceInUrl(tdb, url, lrg->ncbiAcc, TRUE); + char *idUrl = replaceInUrl(url, lrg->ncbiAcc, cart, database, seqName, winStart, + winEnd, tdb->track, TRUE); printf("%s
\n", idUrl, lrg->ncbiAcc); } else printf("%s
\n", lrg->ncbiAcc); printf("Creation Date: %s
\n", lrg->creationDate); char *assemblyDate = hFreezeDate(database); if (isNotEmpty(lrg->mismatches)) { printf("
Mismatches between %s and %s assembly sequence:
\n", lrg->name, assemblyDate); struct lrgDiff *mismatches = lrgParseMismatches(lrg); printLrgDiffs(lrg, mismatches); } if (isNotEmpty(lrg->indels)) { printf("
Insertions/deletions between %s and %s assembly sequence:
\n", lrg->name, assemblyDate); struct lrgDiff *indels = lrgParseIndels(lrg); printLrgDiffs(lrg, indels); } } if (!found) { printf("No item '%s' starting at %d\n", emptyForNull(item), start); } lmCleanup(&lm); printTrackHtml(tdb); } static struct genbankCds *getLrgCds(struct sqlConnection *conn, struct trackDb *tdb, struct psl *psl) { char *cdsTable = trackDbSetting(tdb, "cdsTable"); if (isEmpty(cdsTable) || !hTableExists(database, cdsTable)) return NULL; struct dyString *dy = sqlDyStringCreate("select cds from %s where id = '%s'", cdsTable, psl->qName); char *cdsString = sqlQuickString(conn, dy->string); if (cdsString != NULL) { struct genbankCds *cds; AllocVar(cds); // Trash cdsString while parsing out start..end: char *startString = cdsString, *endString = strchr(cdsString, '.'); if (endString == NULL || endString[1] != '.' || !isdigit(endString[2])) errAbort("getLrgCds: can't parse cdsString '%s' for %s", cdsString, psl->qName); *endString++ = '\0'; endString++; cds->start = sqlUnsigned(startString) - 1; cds->end = sqlUnsigned(endString); cds->startComplete = TRUE; cds->endComplete = TRUE; cds->complement = (psl->strand[0] == '-'); return cds; } return NULL; } void htcLrgCdna(char *item) /* Serve up LRG transcript cdna seq */ { cartHtmlStart("LRG Transcript Sequence"); char *pslTable = cartString(cart, "table"); struct trackDb *tdb = hashFindVal(trackHash, pslTable); char *cdnaTable = trackDbSetting(tdb, "cdnaTable"); if (isEmpty(cdnaTable) || !hTableExists(database, cdnaTable)) errAbort("htcLrgCdna: cdnaTable not found for '%s'", pslTable); struct sqlConnection *conn = hAllocConn(database); struct psl *psl = getAlignments(conn, pslTable, item); struct genbankCds *cds = getLrgCds(conn, tdb, psl); hFreeConn(&conn); struct dnaSeq *seq = hGenBankGetMrna(database, item, cdnaTable); if (seq == NULL) errAbort("htcLrgCdna: no sequence for '%s' in cdnaTable '%s'", item, cdnaTable); tolowers(seq->dna); if (cds != NULL) toUpperN(seq->dna + cds->start, cds->end - cds->start); printf("
");
 printf(">%s\n", item);
 faWriteNext(stdout, NULL, seq->dna, seq->size);
 printf("
"); hFreeConn(&conn); } void doLrgTranscriptPsl(struct trackDb *tdb, char *item) /* Locus Reference Genomic (LRG) transcript mapping and sequences. */ { struct sqlConnection *conn = hAllocConn(database); struct psl *psl = getAlignments(conn, tdb->table, item); struct genbankCds *cds = getLrgCds(conn, tdb, psl); hFreeConn(&conn); genericHeader(tdb, item); char *url = trackDbSetting(tdb, "url"); if (isNotEmpty(url)) { char *lrgName = cloneString(item); // Truncate the "t1" part to get the LRG ID for link: char *p = strchr(lrgName, 't'); if (p) *p = '\0'; char *urlLabel = trackDbSettingOrDefault(tdb, "urlLabel", "LRG Transcript link"); printf("%s ", urlLabel); - char *lrgTUrl = replaceInUrl(tdb, url, lrgName, TRUE); + //char *lrgTUrl = replaceInUrl(tdb, url, lrgName, TRUE); + char *lrgTUrl = replaceInUrl(url, lrgName, cart, database, seqName, winStart, + winEnd, tdb->track, TRUE); printf("%s
\n", lrgTUrl, item); } struct genePred *gp = genePredFromPsl3(psl, cds, genePredAllFlds, genePredPslCdsMod3, -1, -1); printPos(gp->chrom, gp->txStart, gp->txEnd, gp->strand, FALSE, NULL); printf("

Links to %s sequence:

\n", item); printf("\n"); printf("

Alignment of %s to genome assembly:

", item); int start = cartInt(cart, "o"); printAlignments(psl, start, "htcCdnaAli", tdb->table, item); printTrackHtml(tdb); }