types2files["GDNA"].add(filename)
files2types[filename].add("GDNA")
if re.search(regex["NRNA"], filename) and key not in NRNA:
NRNA[key] = row
types2files["NRNA"].add(filename)
files2types[filename].add("NRNA")
if re.search(regex["SDNA"], filename) and key not in SDNA:
SDNA[key] = row
types2files["SDNA"].add(filename)
files2types[filename].add("SDNA")
if re.search(regex["TRNA"], filename) and key not in TRNA:
TRNA[key] = row
types2files["TRNA"].add(filename)
files2types[filename].add("TRNA")
f.close()
progress.done()
if sum(map(len, [GDNA, SDNA, NRNA, TRNA])) == 0:
print("No read counts available for testing", file=sys.stderr)
sys.exit(0)
fatal = False
for f in files2types:
if len(files2types[f]) < 1:
print("Filename %s does not match any read type regular expression." %
(f, ),
file=sys.stderr)
fatal = True
elif len(files2types[f]) > 1:
print(
"Filename %s matches more than one read type regular expression." %
alt = r[snvheaders[3]].strip()
if r.get('INFO:INDEL'):
continue
if len(ref) != 1:
continue
if not re.search(r'^[ACGT](,[ACGT])*$', alt):
continue
# for h in r:
# if r.get(h):
# usedsnvheaders.add(h)
snvkey = (filename, chr, locus, ref, alt)
if snvkey not in snvdata:
snvdata[snvkey] = r
progress.update()
progress.done()
chrreg = ChromLabelRegistry()
for snvfile in snvchroms:
chrreg.add_labels(snvfile,snvchroms[snvfile])
snvdata1 = {}
for (sf, chr, locus, ref, alt), r in snvdata.iteritems():
chrom = chrreg.label2chrom(sf,chr)
assert(chrom)
snvkey = (chrom,locus,ref,alt)
if snvkey not in snvdata1:
snvdata1[snvkey] = (chrom,locus,ref,alt,r)
for bamfile in opt.alignments:
