static void prAlign(struct sqlConnection *conn, char *pslTbl, struct psl *psl)
/* print an alignment */
{
// genomic location
webPrintLinkCellStart();
printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd,
psl->tName, psl->tStart+1, psl->tEnd);
webPrintLinkCellEnd();
// genomic span
webPrintLinkCellRightStart();
printf("%d", psl->tEnd-psl->tStart);
webPrintLinkCellEnd();
// strand
webPrintLinkCell(psl->strand);
// mRNA location, linked to aligment viewer
webPrintLinkCellStart();
char other[128];
safef(other, sizeof(other), "%d&aliTable=%s", psl->tStart, pslTbl);
hgcAnchorSomewhere("htcCdnaAli", psl->qName, other, psl->tName);
printf("%s:%d-%d</A>", psl->qName, psl->qStart+1, psl->qEnd);
webPrintLinkCellEnd();
// identity
webPrintLinkCellRightStart();
printf("%.2f%%", 100.0 * pslIdent(psl));
webPrintLinkCellEnd();
// fraction aligned
webPrintLinkCellRightStart();
int aligned = psl->match + psl->misMatch + psl->repMatch;
printf("%.2f%%", 100.0*aligned/((float)psl->qSize));
webPrintLinkCellEnd();
}
static void prRefSeqSim(struct cloneInfo *ci, struct geneSim *gs)
/* print similarity information for a given RefSeq */
{
webPrintLinkTableNewRow();
// RefSeq acc and link
webPrintLinkCellStart();
printf("<a href=\"");
printEntrezNucleotideUrl(stdout, gs->gene->name);
printf("\" TARGET=_blank>%s</a>", gs->gene->name);
webPrintLinkCellEnd();
// link to browser
webPrintLinkCellStart();
printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\" target=_blank>%s:%d-%d</A>",
hgTracksPathAndSettings(), database,
gs->gene->chrom, gs->gene->txStart+1, gs->gene->txEnd,
gs->gene->chrom, gs->gene->txStart+1, gs->gene->txEnd);
webPrintLinkCellEnd();
// similarity
webPrintLinkCellRightStart();
printf("%0.2f%%", 100.0*gs->sim);
webPrintLinkCellEnd();
}
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);
}
}
