def test_minimal_VCF_definition_io(self):
buf = io.StringIO()
with open(pkg_file('genomvar.test', 'data/example1.vcf'), 'rt') as fh:
for line in fh:
if line.startswith('##fileformat') \
or line.startswith('#CHROM') \
or not line.startswith('#'):
buf.write(line)
buf.seek(0)
reader = VCFReader(buf)
outbuf = io.StringIO()
writer = VCFWriter(format_spec=[RESERVED_FORMAT.GT],
samples=reader.samples)
variants1 = []
for vrt in reader.iter_vrt(parse_samples=True):
self.assertTrue(
isinstance(vrt.attrib['samples']['SAMP1']['GT'], str))
if vrt.attrib['samples']['SAMP1'].get('GT') == '0/1':
vrt.attrib['samples']['SAMP1']['GT'] = (0, 1)
else:
vrt.attrib['samples']['SAMP1']['GT'] = None
outbuf.write(str(writer.get_row(vrt)))
variants1.append(vrt)
variants1.sort(key=lambda v: v.start)
outbuf.seek(0)
variants2 = list(VCFReader(outbuf).iter_vrt())
variants2.sort(key=lambda v: v.start)
for v1, v2 in zip(variants1, variants2):
self.assertTrue(v1.edit_equal(v2))
def test_example3(self):
reader = VCFReader(pkg_file('genomvar.test', 'data/example3.vcf'))
self.assertEqual(list(reader.get_chroms(allow_no_index=True)),
['chr1', 'chr2', 'chr10'])
vrt = list(reader.iter_vrt(parse_info=True, parse_samples=True))
self.assertGreater(len(vrt), 0)
v = vrt[3]
self.assertEqual(v.attrib['id'], None)
def test_iter_vrt_gzipped(self):
reader = VCFReader(pkg_file('genomvar.test', 'data/example2.vcf.gz'),
index=True)
self.assertEqual(list(reader.chroms), ['chr23', 'chr24'])
for vrt in reader.iter_vrt():
self.assertIn(vrt.chrom, ['chr24', 'chr23'])
self.assertEqual(len(list(reader.find_vrt(chrom='chr24'))), 4)
self.assertEqual(len(list(reader.find_vrt('chr23', 7464, 7465))), 3)
def test_sv_types(self):
reader = VCFReader(pkg_file('genomvar.test', 'data/example4.vcf.gz'))
with warnings.catch_warnings(record=True) as wrn:
# warnings.simplefilter(append=True)
for cnt, vrt in enumerate(reader.iter_vrt()):
pass
self.assertEqual(cnt, 99)
self.assertGreater(len(wrn), 1)
self.assertIn('Structural', str(wrn[-1].message))
def test_check_getting_vrt_is_sorted(self):
reader = VCFReader(pkg_file('genomvar.test',
'data/example_gnomad_2.vcf.gz'),
index=True)
starts = [v.start for v in reader.iter_vrt()]
self.assertEqual(starts, sorted(starts))
starts2 = [
v.start for v in reader.find_vrt('chr15', 74719587, 74824401)
]
self.assertEqual(starts2, sorted(starts2))
def test_from_variants_with_attributes(self):
reader = VCFReader(pkg_file('genomvar.test', 'data/example1.vcf'))
vset = VariantSet.from_variants(list(reader.iter_vrt(parse_info=True)))
vrt = list(vset.find_vrt('chr24', 1200, 1210))
self.assertEqual(len(vrt), 2)
v1 = vrt[0]
self.assertEqual(v1.attrib['info']['NSV'], 1)
self.assertEqual(v1.attrib['id'], '5')
v2 = vrt[1]
self.assertEqual(v2.attrib['id'], None)
recs = vset.to_records()
self.assertEqual(recs[0]['attrib']['info']['NSV'], 2)
def test_from_vcf_missing_values(self):
buf = io.StringIO()
format_fields = (RESERVED_FORMAT.AD, RESERVED_FORMAT.DP,
RESERVED_FORMAT.GT)
header = vcf_header.render(
samples=['S1','S2'],
ctg_len={},
format=[{k:getattr(spec, k.upper()) for k in \
('name', 'number', 'type', 'description')} \
for spec in format_fields])
buf.write(header)
buf.write('chr15\t17017413\t.\tA\tG\t38\t.\t.\tGT\t./.\t0/1\n')
buf.write('chr15\t17017413\t.\tA\tG\t38\t.\t.\tGT:AD\t./.\t0/1:10,.\n')
buf.write('chr15\t17017413\t.\tA\tG\t38\t.\t.\tGT:DP\t./.\t1/1:.\n')
buf.seek(0)
buf.seek(0)
vs = VCFReader(buf)
v = list(vs.iter_vrt(parse_samples=True))[0]
self.assertEqual(v.attrib['samples']['S1']['GT'], (None, None))
def test_to_vcf_row_from_file(self):
def _split_multiallelic(rows):
for row in rows:
for alt in row.ALT.split(','):
kwds = {f:getattr(row,f) for f in VCF_FIELDS}
kwds['ALT'] = alt
kwds['INFO'] = '.'
kwds['FORMAT'] = None
kwds['SAMPLES'] = None
yield str(VCFRow(**kwds))
reader = VCFReader(pkg_file('genomvar.test','data/example1.vcf'))
variants = list(reader.iter_vrt(
parse_info=False,parse_samples=False))
rows = [str(self.writer.get_row(v)) for v in variants]
for r1, r2 in zip(
_split_multiallelic(reader.iter_rows()), rows):
if 'AG\tAGG' in r1: # stripping
continue
self.assertEqual(r1,r2)
reader.close()
def test_iter_vrt_example1(self):
reader = VCFReader(pkg_file('genomvar.test', 'data/example1.vcf'))
self.assertEqual(reader.samples, ['SAMP1'])
vrts = list(reader.iter_vrt(parse_info=True, parse_samples=True))
vrt1, vrt2 = vrts[:2]
# Test Ref and Alt
self.assertEqual([vrt1.start, vrt1.ref, vrt1.alt], [23, 'G', ''])
self.assertEqual([vrt2.start, vrt2.ref, vrt2.alt], [24, '', 'G'])
# Check row numbers
self.assertEqual(vrt1.attrib['vcf_notation']['row'], 0)
self.assertEqual(vrt2.attrib['vcf_notation']['row'], 0)
self.assertEqual(vrt1.attrib['allele_num'], 0)
self.assertEqual(vrt2.attrib['allele_num'], 1)
# Test INFO
self.assertEqual(vrt1.attrib['info']['AF'], 0.5)
self.assertEqual(vrt2.attrib['info']['AF'], 0.5)
# Test SAMPLES fields
self.assertEqual(vrt1.attrib['samples']['SAMP1']['GT'], (0, 1, 0))
self.assertEqual(vrt2.attrib['samples']['SAMP1']['GT'], (0, 0, 1))
def test_change_of_attributes(self):
reader = VCFReader(
pkg_file('genomvar.test','data/example1.vcf'))
vrt = list(reader.iter_vrt())[0]
self.assertEqual(str(self.writer.get_row(vrt)),
'chr24\t23\t1\tAG\tA\t100\tPASS\t.')
vrt2 = copy.deepcopy(vrt)
vrt2.attrib['id'] = '.'
vrt2.attrib['qual'] = '.'
vrt2.attrib['filter'] = '.'
self.assertEqual(str(self.writer.get_row(vrt2)),
'chr24\t23\t.\tAG\tA\t.\t.\t.')
self.assertEqual(str(self.writer.get_row(vrt2, id='.', qual='.', filter='.')),
'chr24\t23\t.\tAG\tA\t.\t.\t.')
vrt3 = copy.deepcopy(vrt)
vrt3.attrib['id'] = None
vrt3.attrib['qual'] = None
vrt3.attrib['filter'] = None
self.assertEqual(str(self.writer.get_row(vrt3)),
'chr24\t23\t.\tAG\tA\t.\t.\t.')
reader.close()
reader.close()