static void wrapHgGeneLink(struct sqlConnection *conn, char *name, char *label, char *geneTable) /* Wrap label with link to hgGene if possible. */ { char query[256]; struct sqlResult *sr; char **row; int rowOffset = hOffsetPastBin(database, seqName, "sgdGene"); sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", geneTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct genePred *gp = genePredLoad(row+rowOffset); printf("<A HREF=\"../cgi-bin/hgGene?db=%s", database); printf("&hgg_gene=%s", gp->name); printf("&hgg_chrom=%s", gp->chrom); printf("&hgg_start=%d", gp->txStart); printf("&hgg_end=%d", gp->txEnd); printf("\">"); printf("%s", label); printf("</A>"); } else printf("%s", label); sqlFreeResult(&sr); }
void doTriangle(struct trackDb *tdb, char *item, char *motifTable) /* Display detailed info on a regulatory triangle item. */ { int start = cartInt(cart, "o"); struct dnaSeq *seq = NULL; struct dnaMotif *motif = loadDnaMotif(item, motifTable); char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); char query[256]; struct sqlResult *sr; char **row; struct bed *hit = NULL; struct sqlConnection *conn = hAllocConn(database); cartWebStart(cart, database, "Regulatory Motif Info"); genericBedClick(conn, tdb, item, start, 6); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) hit = bedLoadN(row + rowOffset, 6); sqlFreeResult(&sr); if (hit != NULL) { seq = hDnaFromSeq(database, hit->chrom, hit->chromStart, hit->chromEnd, dnaLower); if (hit->strand[0] == '-') reverseComplement(seq->dna, seq->size); } motifHitSection(seq, motif); printTrackHtml(tdb); }
void doPeakClusters(struct trackDb *tdb, char *item) /* Display detailed info about a cluster of DNase peaks from other tracks. */ { int start = cartInt(cart, "o"); char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); char query[256]; struct sqlResult *sr; char **row; struct bed *cluster = NULL; struct sqlConnection *conn = hAllocConn(database); cartWebStart(cart, database, "%s item details", tdb->shortLabel); sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) cluster = bedLoadN(row+rowOffset, 5); sqlFreeResult(&sr); if (cluster != NULL) { /* Get list of subgroups to display */ char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay"); if (inputTableFieldDisplay != NULL) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); /* Print out some information about the cluster overall. */ printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, sqlRowCount(conn, sqlCheckIdentifier(inputTrackTable))); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); /* In a new section put up list of hits. */ webNewSection("List of Items in Cluster"); webPrintLinkTableStart(); printClusterTableHeader(fieldList, FALSE, FALSE, TRUE); printPeakClusterInfo(tdb, cart, conn, inputTrackTable, fieldList, cluster); } else errAbort("Missing required trackDb setting %s for track %s", "inputTableFieldDisplay", tdb->track); webPrintLinkTableEnd(); } printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(), tdb->track); printf("List all items assayed"); printf("</A><BR>\n"); webNewSection("Track Description"); printTrackHtml(tdb); hFreeConn(&conn); }
void doTransRegCode(struct trackDb *tdb, char *item, char *motifTable) /* Display detailed info on a transcriptional regulatory code item. */ { struct dnaMotif *motif = loadDnaMotif(item, motifTable); int start = cartInt(cart, "o"); struct dnaSeq *seq = NULL; char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); char query[256]; struct sqlResult *sr; char **row; struct sqlConnection *conn = hAllocConn(database); struct transRegCode *trc = NULL; cartWebStart(cart, database, "Regulatory Code Info"); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) trc = transRegCodeLoad(row+rowOffset); sqlFreeResult(&sr); if (trc != NULL) { char strand[2]; seq = hDnaFromSeq(database, trc->chrom, trc->chromStart, trc->chromEnd, dnaLower); if (seq->size != motif->columnCount) { printf("WARNING: seq->size = %d, motif->colCount=%d<BR>\n", seq->size, motif->columnCount); strand[0] = '?'; seq = NULL; } else { strand[0] = dnaMotifBestStrand(motif, seq->dna); if (strand[0] == '-') reverseComplement(seq->dna, seq->size); } strand[1] = 0; printf("<B>Name:</B> "); sacCerHgGeneLinkName(conn, trc->name); printf("<BR>\n"); printf("<B>ChIP-chip Evidence:</B> %s<BR>\n", trc->chipEvidence); printf("<B>Species conserved in:</B> %d of 2<BR>\n", trc->consSpecies); if (seq != NULL) printf("<B>Bit Score of Motif Hit:</B> %4.2f<BR>\n", dnaMotifBitScore(motif, seq->dna)); printf("<B>Item score:</B> %d<BR>\n", trc->score); printPosOnChrom(trc->chrom, trc->chromStart, trc->chromEnd, strand, TRUE, trc->name); } motifHitSection(seq, motif); printTrackHtml(tdb); }
static void getAligns(struct sqlConnection *conn, struct hash *refSeqVerInfoTbl, char *outFile) /* get request alignments from database */ { int off = hOffsetPastBin(sqlGetDatabase(conn), NULL, "refSeqAli"); struct sqlResult *sr = sqlGetResult(conn, "SELECT * FROM refSeqAli"); FILE *fh = mustOpen(outFile, "w"); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row+off); processPsl(fh, refSeqVerInfoTbl, psl); pslFree(&psl); } carefulClose(&fh); sqlFreeResult(&sr); }
void getSeqGapsUnsplit(struct sqlConnection *conn, struct hash *chromHash) /* Return a tree of ranges for sequence gaps in all chromosomes, * assuming an unsplit gap table -- when the table is unsplit, it's * probably for a scaffold assembly where we *really* don't want * to do one query per scaffold! */ { struct rbTreeNode **stack = lmAlloc(qLm, 256 * sizeof(stack[0])); struct rbTree *tree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack); int rowOffset = hOffsetPastBin(sqlGetDatabase(conn), NULL, "gap"); struct sqlResult *sr; char **row; char *prevChrom = NULL; sr = sqlGetResult(conn, "NOSQLINJ select * from gap order by chrom"); while ((row = sqlNextRow(sr)) != NULL) { struct agpGap gap; struct simpleRange *range; agpGapStaticLoad(row+rowOffset, &gap); if (prevChrom == NULL) prevChrom = cloneString(gap.chrom); else if (! sameString(prevChrom, gap.chrom)) { setNGap(prevChrom, chromHash, tree); freeMem(prevChrom); stack = lmAlloc(qLm, 256 * sizeof(stack[0])); tree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack); prevChrom = cloneString(gap.chrom); } lmAllocVar(tree->lm, range); range->start = gap.chromStart; range->end = gap.chromEnd; rbTreeAdd(tree, range); } if (prevChrom != NULL) { setNGap(prevChrom, chromHash, tree); freeMem(prevChrom); } sqlFreeResult(&sr); }
void intronSizes(char *database, char *table) /* intronSizes - Output list of intron sizes.. */ { struct dyString *query = newDyString(1024); struct sqlConnection *conn; struct sqlResult *sr; char **row; struct genePred *gp; int rowOffset; struct bed *bedList = NULL, *bed = NULL; hSetDb(database); rowOffset = hOffsetPastBin(NULL, table); conn = hAllocConn(database); sqlDyStringPrintf(query, "select * from %s", table); if (chromName != NULL) dyStringPrintf(query, " where chrom = '%s'", chromName); if (cgiBoolean("withUtr")) { dyStringPrintf(query, " %s txStart != cdsStart", (chromName == NULL ? "where" : "and")); } sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { gp = genePredLoad(row+rowOffset); genePredIntrons(gp, &bedList); slReverse(&bedList); for (bed = bedList ; bed != NULL ; bed=bed->next) bedTabOutN(bed,6, stdout); bedFreeList(&bedList); genePredFree(&gp); } sqlFreeResult(&sr); hFreeConn(&conn); }
void intronEnds(char *database, char *table) /* intronEnds - Gather stats on intron ends.. */ { struct dyString *query = newDyString(1024); struct sqlConnection *conn; struct sqlResult *sr; char **row; struct genePred *gp; int total = 0; int gtag = 0; int gcag = 0; int atac = 0; int ctac = 0; DNA ends[4]; int exonIx, txStart; struct dnaSeq *seq; int rowOffset; char strand; rowOffset = hOffsetPastBin(database, NULL, table); conn = hAllocConn(database); sqlDyStringPrintf(query, "select * from %s", table); if (chromName != NULL) dyStringPrintf(query, " where chrom = '%s'", chromName); if (cgiBoolean("withUtr")) { dyStringPrintf(query, " %s txStart != cdsStart", (chromName == NULL ? "where" : "and")); } sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { gp = genePredLoad(row+rowOffset); strand = gp->strand[0]; txStart = gp->txStart; seq = hDnaFromSeq(database, gp->chrom, txStart, gp->txEnd, dnaLower); for (exonIx=1; exonIx < gp->exonCount; ++exonIx) { ++total; memcpy(ends, seq->dna + gp->exonEnds[exonIx-1] - txStart, 2); memcpy(ends+2, seq->dna + gp->exonStarts[exonIx] - txStart - 2, 2); if (strand == '-') reverseComplement(ends, 4); if (ends[0] == 'g' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'g') ++gtag; if (ends[0] == 'g' && ends[1] == 'c' && ends[2] == 'a' && ends[3] == 'g') ++gcag; if (ends[0] == 'a' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'c') ++atac; if (ends[0] == 'c' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'c') ++ctac; } freeDnaSeq(&seq); genePredFree(&gp); } sqlFreeResult(&sr); hFreeConn(&conn); printf("gt/ag %d (%4.2f)\n", gtag, 100.0*gtag/total); printf("gc/ag %d (%4.2f)\n", gcag, 100.0*gcag/total); printf("at/ac %d (%4.2f)\n", atac, 100.0*atac/total); printf("ct/ac %d (%4.2f)\n", ctac, 100.0*ctac/total); printf("Total %d\n", total); }
void loadSimpleBed(struct track *tg) /* Load the items in one track - just move beds in * window... */ { struct bed *(*loader)(char **row); struct bed *bed, *list = NULL; char **row; int rowOffset; char *words[3]; int wordCt; char query[128]; char *setting = NULL; bool doScoreCtFilter = FALSE; int scoreFilterCt = 0; char *topTable = NULL; if (tg->bedSize <= 3) loader = bedLoad3; else if (tg->bedSize == 4) loader = bedLoad; else if (tg->bedSize == 5) loader = bedLoad5; else loader = bedLoad6; // pairedTagAlign loader is required for base coloring using sequence from seq1 & seq2 // after removing optional bin column, this loader assumes seq1 and seq2 are in // row[6] and row[7] respectively of the sql result. if ((setting = trackDbSetting(tg->tdb, BASE_COLOR_USE_SEQUENCE)) && sameString(setting, "seq1Seq2")) loader = bedLoadPairedTagAlign; /* limit to a specified count of top scoring items. * If this is selected, it overrides selecting item by specified score */ if ((setting = trackDbSettingClosestToHome(tg->tdb, "filterTopScorers")) != NULL) { wordCt = chopLine(cloneString(setting), words); if (wordCt >= 3) { doScoreCtFilter = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, "filterTopScorersOn",sameString(words[0], "on")); scoreFilterCt = cartUsualIntClosestToHome(cart, tg->tdb, FALSE, "filterTopScorersCt", atoi(words[1])); topTable = words[2]; /* if there are not too many rows in the table then can define */ /* top table as the track or subtrack table */ if (sameWord(topTable, "self")) topTable = cloneString(tg->table); } } /* Get list of items */ if (tg->isBigBed) { // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks char *scoreFilter = cartOrTdbString(cart, tg->tdb, "scoreFilter", NULL); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, winStart, winEnd, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; int minScore = 0; if (scoreFilter) minScore = atoi(scoreFilter); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); bed = loader(bedRow); if (scoreFilter == NULL || bed->score >= minScore) slAddHead(&list, bed); } lmCleanup(&lm); } else { struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb); struct sqlResult *sr = NULL; /* limit to items above a specified score */ char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL); if (doScoreCtFilter && (topTable != NULL) && hTableExists(database, topTable)) { sqlSafef(query, sizeof(query),"select * from %s order by score desc limit %d", topTable, scoreFilterCt); sr = sqlGetResult(conn, query); rowOffset = hOffsetPastBin(database, hDefaultChrom(database), topTable); } else if(scoreFilterClause != NULL && tg->bedSize >= 5) { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, scoreFilterClause, &rowOffset); } else { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); } freeMem(scoreFilterClause); while ((row = sqlNextRow(sr)) != NULL) { bed = loader(row+rowOffset); slAddHead(&list, bed); } sqlFreeResult(&sr); hFreeConn(&conn); } if (doScoreCtFilter) { /* filter out items not in this window */ struct bed *newList = bedFilterListInRange(list, NULL, chromName, winStart, winEnd); list = newList; } slReverse(&list); tg->items = list; }
void doGvf(struct trackDb *tdb, char *item) /* Show details for variants represented as GVF, stored in a bed8Attrs table */ { struct sqlConnection *conn = hAllocConn(database); int start = cartInt(cart, "o"); char query[1024]; sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); struct sqlResult *sr = sqlGetResult(conn, query); char **row; if ((row = sqlNextRow(sr)) == NULL) errAbort("doGvfDetails: can't find item '%s' in %s at %s:%d", item, database, seqName, start); int rowOffset = hOffsetPastBin(database, seqName, tdb->table); struct bed8Attrs *ba = bed8AttrsLoad(row+rowOffset); bedPrintPos((struct bed *)ba, 3, tdb); int i = 0; // Note: this loop modifies ba->attrVals[i], assuming we won't use them again: for (i = 0; i < ba->attrCount; i++) { // The ID is the bed8Attrs name and has already been displayed: if (sameString(ba->attrTags[i], "ID")) continue; cgiDecode(ba->attrVals[i], ba->attrVals[i], strlen(ba->attrVals[i])); char *tag = ba->attrTags[i]; // User-defined keywords used in dbVar's GVF: if (sameString(tag, "var_type")) // This one isn't anymore, but I add it back (hg18.txt). tag = "Variant type"; else if (sameString(tag, "clinical_int")) tag = "Clinical interpretation"; else if (sameString(tag, "var_origin")) tag = "Variant origin"; else if (islower(tag[0])) // Uppercase for nice display, assuming user doesn't care which keywords are // user-defined vs. GVF standard: tag[0] = toupper(tag[0]); // GVF standard Start_range and End_range tags (1-based coords): if (sameString(tag, "Start_range") || sameString(tag, "End_range")) { char *copy = cloneString(ba->attrVals[i]); char *words[3]; int wordCount = chopCommas(copy, words); if (wordCount == 2 && (sameString(".", words[0]) || isInteger(words[0])) && (sameString(".", words[1]) || isInteger(words[1]))) { boolean isStartRange = sameString(tag, "Start_range"); char *rangeStart = words[0], *rangeEnd = words[1]; if (sameString(".", rangeStart)) rangeStart = "unknown"; if (sameString(".", rangeEnd)) rangeEnd = "unknown"; if (isStartRange) printf("<B>Start range</B>: outer start %s, inner start %s<BR>\n", rangeStart, rangeEnd); else printf("<B>End range</B>: inner end %s, outer end %s<BR>\n", rangeStart, rangeEnd); } else // not formatted as expected, just print as-is: printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i])); } // Parent sounds like mom or dad (as in var_origin)... tweak it too: else if (sameString(tag, "Parent")) { printf("<B>Variant region:</B> " "<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" " "TARGET=_BLANK>%s</A><BR>\n", ba->attrVals[i], htmlEncode(ba->attrVals[i])); } else if (sameString(tag, "Name")) { char *url = trackDbSetting(tdb, "url"); // Show the Name only if it hasn't already appeared in the URL: if (url == NULL || !stringIn("$$", url)) printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i])); } else if (sameWord(tag, "Phenotype_id") && startsWith("HPO:HP:", ba->attrVals[i])) { subChar(tag, '_', ' '); printf("<B>%s</B>: <A HREF=\"http://www.berkeleybop.org/obo/%s\" " "TARGET=_BLANK>%s</A><BR>\n", tag, ba->attrVals[i]+strlen("HPO:"), htmlEncode(ba->attrVals[i])); } else { subChar(tag, '_', ' '); printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i])); } } sqlFreeResult(&sr); hFreeConn(&conn); /* printTrackHtml is done in genericClickHandlerPlus. */ }
void doTransRegCodeProbe(struct trackDb *tdb, char *item, char *codeTable, char *motifTable, char *tfToConditionTable, char *conditionTable) /* Display detailed info on a ChIP-chip probe from transRegCode experiments. */ { char query[256]; struct sqlResult *sr; char **row; int rowOffset = hOffsetPastBin(database, seqName, tdb->table); struct sqlConnection *conn = hAllocConn(database); struct transRegCodeProbe *probe = NULL; cartWebStart(cart, database, "ChIP-chip Probe Info"); sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", tdb->table, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) probe = transRegCodeProbeLoad(row+rowOffset); sqlFreeResult(&sr); if (probe != NULL) { struct tfData *tfList = NULL, *tf; struct hash *tfHash = newHash(0); struct transRegCode *trc; int i; /* Print basic info. */ printf("<B>Name:</B> %s<BR>\n", probe->name); printPosOnChrom(probe->chrom, probe->chromStart, probe->chromEnd, NULL, TRUE, probe->name); /* Make up list of all transcriptionFactors. */ for (i=0; i<probe->tfCount; ++i) { /* Parse out factor and condition. */ char *tfName = probe->tfList[i]; char *condition = strchr(tfName, '_'); struct tfCond *cond; if (condition != NULL) *condition++ = 0; else condition = "n/a"; tf = hashFindVal(tfHash, tfName); if (tf == NULL) { AllocVar(tf); hashAddSaveName(tfHash, tfName, tf, &tf->name); slAddHead(&tfList, tf); } AllocVar(cond); cond->name = cloneString(condition); cond->binding = probe->bindVals[i]; slAddHead(&tf->conditionList, cond); } slSort(&tfList, tfDataCmpName); /* Fold in motif hits in region. */ if (sqlTableExists(conn, codeTable)) { sr = hRangeQuery(conn, codeTable, probe->chrom, probe->chromStart, probe->chromEnd, "chipEvidence != 'none'", &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { trc = transRegCodeLoad(row+rowOffset); tf = hashFindVal(tfHash, trc->name); if (tf != NULL) slAddTail(&tf->trcList, trc); } sqlFreeResult(&sr); } if (tfList == NULL) printf("No significant immunoprecipitation."); else { tfBindLevelSection(tfList, conn, motifTable, tfToConditionTable); } transRegCodeProbeFree(&probe); growthConditionSection(conn, conditionTable); } printf("\n<HR>\n"); printTrackHtml(tdb); hFreeConn(&conn); }