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);
}
}
