void twoBitInfo(char *inName, char *outName)
/* twoBitInfo - get information about sequences in a .2bit file. */
{
struct twoBitFile *tbf;
FILE *outFile;
char *seqName = NULL;
twoBitParseRange(inName, &inName, &seqName, NULL, NULL);
tbf = twoBitOpen(inName);
outFile = mustOpen(outName, "w");
if (seqName != NULL)
{
char *seqArray[1023];
int i;
int seqCount = chopString(seqName, ",", seqArray, ArraySize(seqArray));
for (i = 0 ; i < seqCount ; i++)
{
if (optionExists("maskBed"))
twoBitOutMaskBeds(tbf, seqArray[i], outFile);
else if (optionExists("nBed"))
twoBitOutNBeds(tbf, seqArray[i], outFile);
else if(optionExists("noNs"))
fprintf(outFile, "%s\t%d\n", seqArray[i], twoBitSeqSizeNoNs(tbf, seqArray[i]));
else
fprintf(outFile, "%s\t%d\n", seqArray[i], twoBitSeqSize(tbf, seqArray[i]));
}
}
else
{
struct twoBitIndex *index;
for (index = tbf->indexList; index != NULL; index = index->next)
{
if (optionExists("maskBed"))
twoBitOutMaskBeds(tbf, index->name, outFile);
else if (optionExists("nBed"))
twoBitOutNBeds(tbf, index->name, outFile);
else if(optionExists("noNs"))
fprintf(outFile, "%s\t%d\n", index->name, twoBitSeqSizeNoNs(tbf, index->name));
else
fprintf(outFile, "%s\t%d\n", index->name, twoBitSeqSize(tbf, index->name));
}
}
twoBitClose(&tbf);
carefulClose(&outFile);
}
void mafStats(char *twoBitFile, char *mafDir, char *outFile)
/* mafStats - Calculate basic stats on maf file including species-by-species
* coverage and percent ID. */
{
struct twoBitFile *tbf = twoBitOpen(twoBitFile);
FILE *f = mustOpen(outFile, "w");
struct twoBitIndex *ix;
long genomeSize = 0;
struct hash *speciesHash = hashNew(0);
struct speciesAcc *speciesList = NULL, *species;
for (ix = tbf->indexList; ix != NULL; ix = ix->next)
{
unsigned chromSize = twoBitSeqSizeNoNs(tbf, ix->name);
genomeSize += chromSize;
char mafFileName[PATH_LEN];
safef(mafFileName, sizeof(mafFileName), "%s/%s.maf", mafDir, ix->name);
struct mafFile *mf = mafMayOpen(mafFileName);
verbose(1, "processing %s\n", ix->name);
if (mf == NULL)
{
warn("%s doesn't exist", mafFileName);
continue;
}
struct mafAli *maf;
while ((maf = mafNext(mf)) != NULL)
{
struct mafComp *mc;
for (mc = maf->components; mc != NULL; mc = mc->next)
{
if (mc->text != NULL)
toUpperN(mc->text, maf->textSize);
}
addCounts(maf, speciesHash, &speciesList);
mafAliFree(&maf);
}
mafFileFree(&mf);
}
slReverse(&speciesList);
for (species = speciesList; species != NULL; species = species->next)
{
fprintf(f, "counts: %s\t%ld\t%ld\t%ld\n", species->name, species->covCount, species->aliCount, species->idCount);
fprintf(f, "precents: %s\t%4.2f%%\t%4.2f%%\t%4.2f%%\n",
species->name, 100.0 * species->covCount/genomeSize,
100.0 * species->aliCount/genomeSize,
100.0 * species->idCount/species->aliCount);
}
carefulClose(&f);
}
