void twoBitToFa(char *inName, char *outName)
/* twoBitToFa - Convert all or part of twoBit file to fasta. */
{
struct twoBitFile *tbf;
FILE *outFile = mustOpen(outName, "w");
struct twoBitSpec *tbs;
if (clSeq != NULL)
{
char seqSpec[2*PATH_LEN];
if (clEnd > clStart)
safef(seqSpec, sizeof(seqSpec), "%s:%s:%d-%d", inName, clSeq, clStart, clEnd);
else
safef(seqSpec, sizeof(seqSpec), "%s:%s", inName, clSeq);
tbs = twoBitSpecNew(seqSpec);
}
else if (clSeqList != NULL)
tbs = twoBitSpecNewFile(inName, clSeqList);
else
tbs = twoBitSpecNew(inName);
if (tbs == NULL)
errAbort("%s is not a twoBit file", inName);
if (tbs->seqs != NULL && clBpt != NULL)
tbf = twoBitOpenExternalBptIndex(tbs->fileName, clBpt);
else
tbf = twoBitOpen(tbs->fileName);
if (clBed != NULL)
{
processSeqsFromBed(tbf, clBed, outFile);
}
else
{
if (tbs->seqs == NULL)
processAllSeqs(tbf, outFile);
else
processSeqSpecs(tbf, tbs->seqs, outFile);
}
twoBitSpecFree(&tbs);
carefulClose(&outFile);
twoBitClose(&tbf);
}
void searchOneIndex(int fileCount, char *files[], struct genoFind *gf, char *outName,
boolean isProt, struct hash *maskHash, FILE *outFile, boolean showStatus)
/* Search all sequences in all files against single genoFind index. */
{
int i;
char *fileName;
int count = 0;
long long totalSize = 0;
gfOutputHead(gvo, outFile);
for (i=0; i<fileCount; ++i)
{
fileName = files[i];
if (nibIsFile(fileName))
{
struct dnaSeq *seq;
if (isProt)
errAbort("%s: Can't use .nib files with -prot or d=prot option\n", fileName);
seq = nibLoadAllMasked(NIB_MASK_MIXED, fileName);
freez(&seq->name);
seq->name = cloneString(fileName);
searchOneMaskTrim(seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
freeDnaSeq(&seq);
}
else if (twoBitIsSpec(fileName))
{
struct twoBitSpec *tbs = twoBitSpecNew(fileName);
struct twoBitFile *tbf = twoBitOpen(tbs->fileName);
if (isProt)
errAbort("%s is a two bit file, which doesn't work for proteins.",
fileName);
if (tbs->seqs != NULL)
{
struct twoBitSeqSpec *ss = NULL;
for (ss = tbs->seqs; ss != NULL; ss = ss->next)
{
struct dnaSeq *seq = twoBitReadSeqFrag(tbf, ss->name,
ss->start, ss->end);
searchOneMaskTrim(seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
dnaSeqFree(&seq);
}
}
else
{
struct twoBitIndex *index = NULL;
for (index = tbf->indexList; index != NULL; index = index->next)
{
struct dnaSeq *seq = twoBitReadSeqFrag(tbf, index->name, 0, 0);
searchOneMaskTrim(seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
dnaSeqFree(&seq);
}
}
twoBitClose(&tbf);
}
else
{
static struct dnaSeq seq;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
searchOneMaskTrim(&seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
}
lineFileClose(&lf);
}
}
carefulClose(&outFile);
if (showStatus)
printf("Searched %lld bases in %d sequences\n", totalSize, count);
}
