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 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); }
void doFlyreg(struct trackDb *tdb, char *item) /* flyreg.org: Drosophila DNase I Footprint db. */ { struct dyString *query = newDyString(256); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin = FALSE; char *motifTable = "flyregMotif"; struct dnaMotif *motif = NULL; boolean isVersion2 = sameString(tdb->table, "flyreg2"); genericHeader(tdb, item); if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin)) errAbort("track %s not found", tdb->table); sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ", fullTable, seqName); hAddBinToQuery(start, end, query); sqlDyStringPrintf(query, "chromStart = %d and name = '%s'", start, item); sr = sqlGetResult(conn, query->string); if ((row = sqlNextRow(sr)) != NULL) { struct flyreg2 fr; if (isVersion2) flyreg2StaticLoad(row+hasBin, &fr); else flyregStaticLoad(row+hasBin, (struct flyreg *)(&fr)); printf("<B>Factor:</B> %s<BR>\n", fr.name); printf("<B>Target:</B> %s<BR>\n", fr.target); if (isVersion2) printf("<B>Footprint ID:</B> %06d<BR>\n", fr.fpid); printf("<B>PubMed ID:</B> <A HREF=\""); printEntrezPubMedUidUrl(stdout, fr.pmid); printf("\" TARGET=_BLANK>%d</A><BR>\n", fr.pmid); bedPrintPos((struct bed *)(&fr), 3, tdb); if (hTableExists(database, motifTable)) { motif = loadDnaMotif(item, motifTable); if (motif != NULL) motifHitSection(NULL, motif); } } else errAbort("query returned no results: \"%s\"", query->string); dyStringFree(&query); sqlFreeResult(&sr); hFreeConn(&conn); if (motif != NULL) webNewSection("%s",tdb->longLabel); printTrackHtml(tdb); }
static double motifScoreHere(char *chrom, int start, int end, char *motifName, char *motifTable) /* Return score of motif at given position. */ { double score; struct dnaSeq *seq = hDnaFromSeq(database, chrom, start, end, dnaLower); struct dnaMotif *motif = loadDnaMotif(motifName, motifTable); char strand = dnaMotifBestStrand(motif, seq->dna); if (strand == '-') reverseComplement(seq->dna, seq->size); score = dnaMotifBitScore(motif, seq->dna); dnaMotifFree(&motif); dnaSeqFree(&seq); return score; }
void doClusterMotifDetails(struct sqlConnection *conn, struct trackDb *tdb, struct factorSource *cluster) /* Display details about TF binding motif(s) in cluster */ { char *motifTable = trackDbSetting(tdb, "motifTable"); // localizations char *motifPwmTable = trackDbSetting(tdb, "motifPwmTable"); // PWM used to draw sequence logo char *motifMapTable = trackDbSetting(tdb, "motifMapTable"); // map target to motif struct slName *motifNames = NULL, *mn; // list of canonical motifs for the factor struct dnaMotif *motif = NULL; struct bed6FloatScore *hit = NULL, *maxHit = NULL; char **row; char query[256]; if (motifTable != NULL && sqlTableExists(conn, motifTable)) { struct sqlResult *sr; int rowOffset; char where[256]; if (motifMapTable == NULL || !sqlTableExists(conn, motifMapTable)) { // Assume cluster name is motif name if there is no map table motifNames = slNameNew(cluster->name); } else { sqlSafef(query, sizeof(query), "select motif from %s where target = '%s'", motifMapTable, cluster->name); char *ret = sqlQuickString(conn, query); if (ret == NULL) { // missing target from table -- no canonical motif webNewEmptySection(); return; } motifNames = slNameListFromString(ret, ','); } for (mn = motifNames; mn != NULL; mn = mn->next) { sqlSafefFrag(where, sizeof(where), "name='%s' order by score desc limit 1", mn->name); sr = hRangeQuery(conn, motifTable, cluster->chrom, cluster->chromStart, cluster->chromEnd, where, &rowOffset); if ((row = sqlNextRow(sr)) != NULL) { hit = bed6FloatScoreLoad(row + rowOffset); if (maxHit == NULL || maxHit->score < hit->score) maxHit = hit; } sqlFreeResult(&sr); } } if (maxHit == NULL) { // Maintain table layout webNewEmptySection(); return; } hit = maxHit; webNewSection("Canonical Motif in Cluster"); char posLink[1024]; safef(posLink, sizeof(posLink),"<a href=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a>", hgTracksPathAndSettings(), database, cluster->chrom, hit->chromStart+1, hit->chromEnd, cluster->chrom, hit->chromStart+1, hit->chromEnd); printf("<b>Motif Name:</b> %s<br>\n", hit->name); printf("<b>Motif Score"); printf(":</b> %.2f<br>\n", hit->score); printf("<b>Motif Position:</b> %s<br>\n", posLink); printf("<b>Motif Strand:</b> %c<br>\n", (int)hit->strand[0]); struct dnaSeq *seq = hDnaFromSeq(database, seqName, hit->chromStart, hit->chromEnd, dnaLower); if (seq == NULL) return; if (hit->strand[0] == '-') reverseComplement(seq->dna, seq->size); if (motifPwmTable != NULL && sqlTableExists(conn, motifPwmTable)) { motif = loadDnaMotif(hit->name, motifPwmTable); if (motif == NULL) return; motifLogoAndMatrix(&seq, 1, motif); } }