void motifMultipleHitsSection(struct dnaSeq **seqs, int count, struct dnaMotif *motif, char *title)
/* Print out section about motif, possibly with mutliple occurrences. */
{
// Detect inconsistent motif/pwm tables and suppress confusing display
if (motif != NULL)
{
if (seqs != NULL && motif->columnCount != seqs[0]->size)
{
warn("Motif seq length doesn't match PWM\n");
return;
}
}
webNewSection(title);
motifLogoAndMatrix(seqs, count, motif);
}
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);
}
}
