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 gtfToGenePred(char *gtfFile, char *gpFile, char *infoFile)
/* gtfToGenePred - convert a GTF file to a genePred.. */
{
struct gffFile *gtf = gffRead(gtfFile);
FILE *gpFh, *infoFh = NULL;
struct gffGroup *group;
if (!gtf->isGtf)
errAbort("%s doesn't appear to be a GTF file (GFF not supported by this program)", gtfFile);
gffGroupLines(gtf);
gpFh = mustOpen(gpFile, "w");
if (infoFile != NULL)
{
infoFh = mustOpen(infoFile, "w");
fputs(infoHeader, infoFh);
}
if (!doSimple)
for (group = gtf->groupList; group != NULL; group = group->next)
if (inclGroup(group))
gtfGroupToGenePred(gtf, group, gpFh, infoFh);
carefulClose(&gpFh);
gffFileFree(>f);
}
void gffIntoDatabase(char *database, char *fileName, char *table, int offset)
/* Load a gff file into database. */
{
struct gffFile *gff = gffFileNew("");
struct gffGroup *group;
struct genePred *gpList = NULL, *gp;
FILE *f;
char *tabName = "genePred.tab";
/* Load fixed gff and convert it to genePred. */
gffFileAdd(gff, fileName, 0);
gffGroupLines(gff);
for (group = gff->groupList; group != NULL; group = group->next)
{
gp = genePredFromGroupedGff(gff, group, group->name, "exon",
genePredCdsStatFld|genePredExonFramesFld,
genePredGxfDefaults);
if (gp != NULL)
{
slAddHead(&gpList, gp);
genePredOffset(gp, offset);
}
}
slSort(&gpList, genePredCmp);
/* Create tab-delimited file. */
f = mustOpen(tabName, "w");
for (gp = gpList; gp != NULL; gp = gp->next)
genePredTabOut(gp, f);
carefulClose(&f);
/* Load into database. */
loadIntoDatabase(database, createGenePred, "sanger22", tabName);
}
