def run_genotype_filters(in_fhand,
out_fhand,
gt_filters,
plots_dir=None,
reader_kwargs=None):
if reader_kwargs is None:
reader_kwargs = {}
reader_kwargs['filename'] = 'pyvcf_bug_workaround'
reader_kwargs['compressed'] = False
reader = VCFReader(in_fhand, **reader_kwargs)
templa_reader = VCFReader(StringIO(reader.header))
writer = VCFWriter(out_fhand, template_reader=templa_reader)
for snv in reader.parse_snvs():
for mapper in gt_filters:
snv = mapper(snv)
try:
writer.write_snv(snv)
except IOError, error:
# The pipe could be already closed
if 'Broken pipe' in str(error):
break
else:
raise
def test_vcf_writer(self):
varscan = open(join(TEST_DATA_DIR, 'vari_filter.vcf'))
reader = VCFReader(fhand=varscan)
out_fhand = NamedTemporaryFile()
writer = VCFWriter(out_fhand, reader)
for snv in reader.parse_snvs():
writer.write_snv(snv)
writer.flush()
assert 'CUUC00027_TC01' in open(out_fhand.name).read()
writer.close()
def test_het_unknown(self):
vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t./.\t1/.\t
'''
vcf = StringIO(VCF_HEADER + vcf)
reader = VCFReader(vcf)
snps = list(reader.parse_snvs())
snp = snps[0]
expected = [[0, 0], [0, 0], [0, 0], [0, 0], [1, 1], [1, 1], [],
[1, None]]
assert [call.int_alleles for call in snps[0].calls] == expected
assert snp.num_called == 7
out_fhand = StringIO()
writer = VCFWriter(out_fhand, reader)
for snv in snps:
writer.write_snv(snv)
assert '1/1\t./.\t1/.' in out_fhand.getvalue()
def run_genotype_filters(in_fhand, out_fhand, gt_filters, plots_dir=None, reader_kwargs=None):
if reader_kwargs is None:
reader_kwargs = {}
reader_kwargs["filename"] = "pyvcf_bug_workaround"
reader_kwargs["compressed"] = False
reader = VCFReader(in_fhand, **reader_kwargs)
templa_reader = VCFReader(StringIO(reader.header))
writer = VCFWriter(out_fhand, template_reader=templa_reader)
for snv in reader.parse_snvs():
for mapper in gt_filters:
snv = mapper(snv)
try:
writer.write_snv(snv)
except IOError, error:
# The pipe could be already closed
if "Broken pipe" in str(error):
break
else:
raise