void polyInfo(char *pslFile, char *genoFile, char *estFile, char *outputFile)
/* polyInfo - Collect info on polyAdenylation signals etc. */
{
struct hash *pslHash = NULL;
struct hash *genoHash = loadGeno(genoFile);
static struct dnaSeq est;
struct lineFile *lf = NULL;
FILE *f = NULL;
pslHash = pslIntoHash(pslFile);
lf = lineFileOpen(estFile, TRUE);
f = mustOpen(outputFile, "w");
while (faSpeedReadNext(lf, &est.dna, &est.size, &est.name))
{
struct pslList *pl;
struct psl *psl;
struct estOrientInfo ei;
if ((pl = hashFindVal(pslHash, est.name)) != NULL)
{
for (psl = pl->list; psl != NULL; psl = psl->next)
{
struct dnaSeq *geno = hashMustFindVal(genoHash, psl->tName);
if (psl->tSize != geno->size)
errAbort("psl generated on a different version of the genome");
ZeroVar(&ei);
fillInEstInfo(&ei, &est, geno, psl);
estOrientInfoTabOut(&ei, f);
}
}
}
}
void pslIntronsOnly(char *inPslName, char *genoFile, char *outPslName)
/* pslIntronsOnly - Filter psl files to only include those with introns. */
{
struct lineFile *lf = NULL;
FILE *outFile = NULL;
struct hash *genoHash = loadGeno(genoFile);
struct psl *psl;
int count = 0, intronCount = 0;
lf = pslFileOpen(inPslName);
outFile = mustOpen(outPslName, "w");
while ((psl = pslNext(lf)) != NULL)
{
struct dnaSeq *geno = hashMustFindVal(genoHash, psl->tName);
if (pslHasIntron(psl, geno, 0))
{
++intronCount;
pslTabOut(psl, outFile);
}
pslFree(&psl);
++count;
}
carefulClose(&outFile);
lineFileClose(&lf);
printf("%d of %d in %s have introns\n", intronCount, count, inPslName);
}
