def test_null_mono(self):
# null qualities were written as blank, causing subsequent parse to fail
print os.path.abspath(
os.path.join(os.path.dirname(__file__), 'null_genotype_mono.vcf'))
p = cyvcf.Reader(fh('null_genotype_mono.vcf'))
assert p.samples
out = StringIO()
writer = cyvcf.Writer(out, p)
map(writer.write_record, p)
out.seek(0)
print out.getvalue()
p2 = cyvcf.Reader(out)
rec = p2.next()
assert rec.samples
def use_cyvcf(vcf_file):
""" Not installing (py3 not supported, py2 installs but import doesn't work)
"""
import cyvcf # need to reinstall instead of pyvcf
import gzip
f = gzip.open(vcf_file) if vcf_file.endswith('.gz') else open(vcf_file)
with f as f:
vcf_reader = cyvcf.Reader(f)
vcf_writer = cyvcf.Writer(sys.stdout, vcf_reader)
for rec in vcf_reader:
msi_fail = proc_fields(rec.REF, rec.ALT[0], rec.samples[0]['AF'],
rec.INFO['MSI'])
if msi_fail:
rec.FILTER.append('MSI_FAIL')
vcf_writer.write_record(rec)
def testWrite(self):
reader = cyvcf.Reader(fh('gatk.vcf'))
out = StringIO()
writer = cyvcf.Writer(out, reader)
records = list(reader)
map(writer.write_record, records)
out.seek(0)
reader2 = cyvcf.Reader(out)
self.assertEquals(reader.samples, reader2.samples)
self.assertEquals(reader.formats, reader2.formats)
self.assertEquals(reader.infos, reader2.infos)
for l, r in zip(records, reader2):
self.assertEquals(l.samples, r.samples)