void gffToBed(char *inGff, char *outBed)
/* gffToBed - Convert a gff file (gff1 or gff2) to bed. Not tested with gff3 */
{
struct gffFile *gff = gffRead(inGff);
FILE *f = mustOpen(outBed, "w");
char *exonFeature = bestExonFeature(gff);
gffGroupLines(gff);
separateGroupsByChromosome(gff);
struct gffGroup *group;
for (group = gff->groupList; group != NULL; group = group->next)
{
struct genePred *gp;
if (gff->isGtf)
gp = genePredFromGroupedGtf(gff, group, group->name, FALSE, FALSE);
else
gp = genePredFromGroupedGff(gff, group, group->name, exonFeature, FALSE, FALSE);
if (gp != NULL)
{
assert(gp->txStart == gp->exonStarts[0]);
struct bed *bed = bedFromGenePred(gp);
bedTabOutN(bed, 12, f);
bedFree(&bed);
}
}
carefulClose(&f);
}
static void showMrnaFromGenePred(struct sqlConnection *conn,
char *geneId, char *geneName)
/* Get mRNA sequence for gene from gene prediction. */
{
char *table = genomeSetting("knownGene");
struct sqlResult *sr;
char **row;
char query[256];
boolean hasBin = hIsBinned(sqlGetDatabase(conn), table);
hPrintf("<TT><PRE>");
safef(query, sizeof(query),
"select * from %s where name='%s'"
" and chrom='%s' and txStart=%d and txEnd=%d",
table, geneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gene = genePredLoad(row+hasBin);
struct bed *bed = bedFromGenePred(gene);
struct dnaSeq *seq = hSeqForBed(sqlGetDatabase(conn), bed);
hPrintf(">%s (%s predicted mRNA)\n", geneId, geneName);
writeSeqWithBreaks(stdout, seq->dna, seq->size, 50);
dnaSeqFree(&seq);
bedFree(&bed);
genePredFree(&gene);
}
else
errAbort("Couldn't find %s at %s:%d-%d", geneId,
curGeneChrom, curGeneStart, curGeneEnd);
sqlFreeResult(&sr);
hPrintf("</TT></PRE>");
}
