struct hash *loadGeno(char *genoFile)
/* load genome sequences into a hash. This supports the multi-sequence
* specs of twoBitLoadAll */
{
struct dnaSeq *genos = NULL, *geno;
struct hash *genoHash = hashNew(0);
if (nibIsFile(genoFile))
genos = nibLoadAllMasked(NIB_MASK_MIXED|NIB_BASE_NAME, genoFile);
else if (twoBitIsSpec(genoFile))
genos = twoBitLoadAll(genoFile);
else
genos = faReadDna(genoFile);
while ((geno = slPopHead(&genos)) != NULL)
{
tolowers(geno->dna);
hashAdd(genoHash, geno->name, geno);
}
return genoHash;
}
void twoBitMask(char *inName, char *maskName, char *outName)
/* twoBitMask - apply masking to a .2bit file, creating a new .2bit file. */
{
struct hash *tbHash = hashNew(20);
struct hash *bitmapHash = hashNew(20);
struct twoBit *twoBitList = NULL;
struct twoBit *twoBit = NULL;
FILE *f = NULL;
if (! twoBitIsFile(inName))
{
if (twoBitIsSpec(inName))
errAbort("Sorry, this works only on whole .2bit files, not specs.");
else
errAbort("Input %s does not look like a proper .2bit file.", inName);
}
twoBitList = slurpInput(inName, tbHash, bitmapHash);
/* Read mask data into bitmapHash, store it in twoBits: */
if ((type && endsWith(type, "bed")) || endsWith(maskName, ".bed"))
maskWithBed(maskName, tbHash, bitmapHash);
else if ((type && endsWith(type, "out")) || endsWith(maskName, ".out"))
maskWithOut(maskName, tbHash, bitmapHash);
else
errAbort("Sorry, maskFile must end in \".bed\" or \".out\".");
/* Create a new .2bit file, write it out from twoBits. */
f = mustOpen(outName, "wb");
twoBitWriteHeader(twoBitList, f);
for (twoBit = twoBitList; twoBit != NULL; twoBit = twoBit->next)
{
twoBitWriteOne(twoBit, f);
}
carefulClose(&f);
/* Don't bother freeing twoBitList and hashes here -- just exit. */
}
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);
}
