Example #1
0
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);
}
Example #2
0
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);
}
Example #3
0
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);
}