struct mafFile *mafOpen(char *fileName)
/* Open up a maf file. Squawk and die if there's a problem. */
{
struct mafFile *mf = mafMayOpen(fileName);
if (mf == NULL)
errnoAbort("Couldn't open %s\n", fileName);
return mf;
}
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);
}
