def test_overlapping_three_non_variants(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
non_variant_1 = vcfio.Variant(reference_name='1', start=0, end=10)
non_variant_2 = vcfio.Variant(reference_name='1', start=3, end=5)
non_variant_3 = vcfio.Variant(reference_name='1', start=4, end=9)
call_1 = vcfio.VariantCall('1', [0, 0])
call_2 = vcfio.VariantCall('2', [0, 0])
call_3 = vcfio.VariantCall('3', [0, 0])
non_variant_1.calls.append(call_1)
non_variant_2.calls.append(call_2)
non_variant_3.calls.append(call_3)
expected_1 = vcfio.Variant(reference_name='1', start=0, end=3)
expected_2 = vcfio.Variant(reference_name='1', start=3, end=4)
expected_3 = vcfio.Variant(reference_name='1', start=4, end=5)
expected_4 = vcfio.Variant(reference_name='1', start=5, end=9)
expected_5 = vcfio.Variant(reference_name='1', start=9, end=10)
expected_1.calls.append(call_1)
expected_2.calls.append(call_1)
expected_2.calls.append(call_2)
expected_3.calls.append(call_1)
expected_3.calls.append(call_2)
expected_3.calls.append(call_3)
expected_4.calls.append(call_1)
expected_4.calls.append(call_3)
expected_5.calls.append(call_1)
expected = [expected_1, expected_2, expected_3, expected_4, expected_5]
actual = list(
strategy.get_merged_variants(
[non_variant_1, non_variant_2, non_variant_3]))
self.assertEqual(sorted(actual), sorted(expected))
def test_non_variant_split_by_snp(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
non_variant = vcfio.Variant(reference_name='1', start=0, end=10)
variant = vcfio.Variant(reference_name='1',
start=5,
end=6,
reference_bases='C',
alternate_bases=['A'])
call_1 = vcfio.VariantCall(name='1', genotype=[0, 0])
call_2 = vcfio.VariantCall(name='2', genotype=[1, 0])
non_variant.calls.append(call_1)
variant.calls.append(call_2)
expected_1 = vcfio.Variant(reference_name='1', start=0, end=5)
expected_2 = vcfio.Variant(reference_name='1',
start=5,
end=6,
reference_bases='C',
alternate_bases=['A'])
expected_3 = vcfio.Variant(reference_name='1', start=6, end=10)
expected_1.calls.append(call_1)
expected_2.calls.append(call_1)
expected_2.calls.append(call_2)
expected_3.calls.append(call_1)
actual = list(strategy.get_merged_variants([non_variant, variant]))
expected = [expected_1, expected_2, expected_3]
self.assertEqual(sorted(actual), sorted(expected))
def test_merge_many_different_alternates(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
variant_1 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['C'])
variant_2 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['G'])
variant_3 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['T'])
variant_1.calls.append(
vcfio.VariantCall(name='Sample1', genotype=[1, 0]))
variant_2.calls.append(
vcfio.VariantCall(name='Sample2', genotype=[1, 0]))
variant_3.calls.append(
vcfio.VariantCall(name='Sample3', genotype=[1, 0]))
variants = [variant_1, variant_2, variant_3]
merged_variants = list(strategy.get_merged_variants(variants))
self.assertEqual(sorted(merged_variants), sorted(variants))
def test_get_merged_variants_no_custom_options(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
info_keys_to_move_to_calls_regex=None,
copy_quality_to_calls=False,
copy_filter_to_calls=False)
variants = self._get_sample_variants()
actual = list(strategy.get_merged_variants([variants[0]]))
# Test single variant merge.
self.assertEqual([variants[0]], actual)
# Test multiple variant merge.
merged_variant = list(strategy.get_merged_variants(variants))[0]
self._assert_common_expected_merged_fields(merged_variant)
self.assertEqual(
[vcfio.VariantCall(name='Sample1', genotype=[0, 1],
info={'GQ': 20, 'HQ': [10, 20]}),
vcfio.VariantCall(name='Sample2', genotype=[1, 0],
info={'GQ': 10, 'FLAG1': True}),
vcfio.VariantCall(name='Sample3', genotype=[1, 1]),
vcfio.VariantCall(name='Sample4', genotype=[1, 0], info={'GQ': 20})],
merged_variant.calls)
self.assertItemsEqual(['A1', 'A2', 'A3'], merged_variant.info.keys())
self.assertTrue(
merged_variant.info['A1'] in ('some data', 'some data2'))
self.assertEqual(['data1', 'data2'], merged_variant.info['A2'])
self.assertEqual(['data3', 'data4'], merged_variant.info['A3'])
def test_merge_snp_with_non_variant(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
variant = vcfio.Variant(
reference_name='1',
start=5,
end=6,
reference_bases='A',
alternate_bases=['C'],
names=['v'],
filters=['vf'],
quality=1)
non_variant = vcfio.Variant(
reference_name='1',
start=0,
end=10,
reference_bases='G',
alternate_bases=['<NON_REF>'],
names=['nv'],
filters=['nvf'],
quality=2)
call_1 = vcfio.VariantCall(name='1', genotype=[1, 0])
call_2 = vcfio.VariantCall(name='2', genotype=[0, 0])
variant.calls.append(call_1)
non_variant.calls.append(call_2)
expected_1 = vcfio.Variant(
reference_name='1',
start=0,
end=5,
alternate_bases=['<NON_REF>'],
names=['nv'],
filters=['nvf'],
quality=2)
expected_2 = vcfio.Variant(
reference_name='1',
start=6,
end=10,
alternate_bases=['<NON_REF>'],
names=['nv'],
filters=['nvf'],
quality=2)
expected_3 = vcfio.Variant(
reference_name='1',
start=5,
end=6,
reference_bases='A',
alternate_bases=['C'],
names=['v'],
filters=['vf'],
quality=1)
expected_1.calls.append(call_2)
expected_2.calls.append(call_2)
expected_3.calls.append(call_1)
expected_3.calls.append(call_2)
actual = list(strategy.get_merged_variants([variant, non_variant]))
expected = [expected_1, expected_2, expected_3]
self.assertEqual(sorted(actual), sorted(expected))
def test_get_non_variant_merge_keys(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None, 2)
variant = vcfio.Variant(reference_name='2', start=6, end=12)
keys = strategy.get_merge_keys(variant)
self.assertEqual(next(keys), '2:6')
self.assertEqual(next(keys), '2:8')
self.assertEqual(next(keys), '2:10')
def test_get_merged_variants_move_info_to_calls(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
info_keys_to_move_to_calls_regex='^A1$',
copy_quality_to_calls=False,
copy_filter_to_calls=False)
variants = self._get_sample_variants()
# Test single variant merge.
single_merged_variant = list(
strategy.get_merged_variants([variants[0]]))[0]
self.assertEqual([
vcfio.VariantCall(sample_id=hash_name('Sample1'),
genotype=[0, 1],
info={
'GQ': 20,
'HQ': [10, 20],
'A1': 'some data'
}),
vcfio.VariantCall(sample_id=hash_name('Sample2'),
genotype=[1, 0],
info={
'GQ': 10,
'FLAG1': True,
'A1': 'some data'
})
], single_merged_variant.calls)
# Test multiple variant merge.
merged_variant = list(strategy.get_merged_variants(variants))[0]
self._assert_common_expected_merged_fields(merged_variant)
self.assertEqual([
vcfio.VariantCall(sample_id=hash_name('Sample1'),
genotype=[0, 1],
info={
'GQ': 20,
'HQ': [10, 20],
'A1': 'some data'
}),
vcfio.VariantCall(sample_id=hash_name('Sample2'),
genotype=[1, 0],
info={
'GQ': 10,
'FLAG1': True,
'A1': 'some data'
}),
vcfio.VariantCall(sample_id=hash_name('Sample3'),
genotype=[1, 1],
info={'A1': 'some data2'}),
vcfio.VariantCall(sample_id=hash_name('Sample4'),
genotype=[1, 0],
info={
'GQ': 20,
'A1': 'some data2'
})
], merged_variant.calls)
self.assertItemsEqual(['A2', 'A3'], merged_variant.info.keys())
self.assertEqual(['data1', 'data2'], merged_variant.info['A2'])
self.assertEqual(['data3', 'data4'], merged_variant.info['A3'])
def test_get_snp_merge_keys(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None, 2)
variant_1 = vcfio.Variant(reference_name='1', start=3, end=4)
variant_2 = vcfio.Variant(reference_name='2', start=4, end=5)
self.assertEqual(next(strategy.get_merge_keys(variant_1)), '1:2')
self.assertEqual(next(strategy.get_merge_keys(variant_2)), '2:4')
def test_merge_2_non_variants(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
non_variant_1 = vcfio.Variant(
reference_name='1',
start=0,
end=10,
alternate_bases=['<NON_REF>'],
names=['nonv1', 'nonv2'],
filters=['f1', 'f2'],
quality=1)
non_variant_2 = vcfio.Variant(
reference_name='1',
start=5,
end=15,
alternate_bases=['<NON_REF>'],
names=['nonv2', 'nonv3'],
filters=['f2', 'f3'],
quality=2)
call_1 = vcfio.VariantCall(name='1', genotype=[0, 0])
call_2 = vcfio.VariantCall(name='2', genotype=[0, 0])
non_variant_1.calls.append(call_1)
non_variant_2.calls.append(call_2)
expected_1 = vcfio.Variant(
reference_name='1',
start=0,
end=5,
alternate_bases=['<NON_REF>'],
names=['nonv1', 'nonv2'],
filters=['f1', 'f2'],
quality=1)
expected_2 = vcfio.Variant(
reference_name='1',
start=10,
end=15,
alternate_bases=['<NON_REF>'],
names=['nonv2', 'nonv3'],
filters=['f2', 'f3'],
quality=2)
expected_3 = vcfio.Variant(
reference_name='1',
start=5,
end=10,
alternate_bases=['<NON_REF>'],
names=['nonv1', 'nonv2', 'nonv3'],
filters=['f1', 'f2', 'f3'],
quality=1)
expected_1.calls.append(call_1)
expected_2.calls.append(call_2)
expected_3.calls.append(call_1)
expected_3.calls.append(call_2)
actual = list(strategy.get_merged_variants([non_variant_1, non_variant_2]))
expected = [expected_1, expected_2, expected_3]
self.assertEqual(sorted(actual), sorted(expected))
def test_align_non_variant(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None, 2)
non_variant = vcfio.Variant(reference_name='1', start=5, end=12)
expected = copy.deepcopy(non_variant)
expected.start = 8
expected.end = 10
actual = list(strategy.get_merged_variants([non_variant], '1:8'))
self.assertEqual(actual, [expected])
def test_get_merged_variants_move_everything_to_calls(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
info_keys_to_move_to_calls_regex='.*',
copy_quality_to_calls=True,
copy_filter_to_calls=True)
variants = self._get_sample_variants()
# Test single variant merge.
single_merged_variant = list(strategy.get_merged_variants([variants[0]]))[0]
self.assertEqual(
[vcfio.VariantCall(name='Sample1', genotype=[0, 1],
info={'GQ': 20, 'HQ': [10, 20],
'A1': 'some data', 'A2': ['data1', 'data2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS']}),
vcfio.VariantCall(name='Sample2', genotype=[1, 0],
info={'GQ': 10, 'FLAG1': True,
'A1': 'some data', 'A2': ['data1', 'data2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS']})],
single_merged_variant.calls)
merged_variant = list(strategy.get_merged_variants(variants))[0]
self._assert_common_expected_merged_fields(merged_variant)
self.assertEqual(
[vcfio.VariantCall(name='Sample1', genotype=[0, 1],
info={'GQ': 20, 'HQ': [10, 20],
'A1': 'some data', 'A2': ['data1', 'data2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS']}),
vcfio.VariantCall(name='Sample2', genotype=[1, 0],
info={'GQ': 10, 'FLAG1': True,
'A1': 'some data', 'A2': ['data1', 'data2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS']}),
vcfio.VariantCall(name='Sample3', genotype=[1, 1],
info={'A1': 'some data2', 'A3': ['data3', 'data4'],
ColumnKeyConstants.QUALITY: 20,
ColumnKeyConstants.FILTER: ['q10']}),
vcfio.VariantCall(name='Sample4', genotype=[1, 0],
info={'GQ': 20,
'A1': 'some data2', 'A3': ['data3', 'data4'],
ColumnKeyConstants.QUALITY: 20,
ColumnKeyConstants.FILTER: ['q10']})],
merged_variant.calls)
self.assertEqual([], merged_variant.info.keys())
def test_merge_one_overlap(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
variant_1 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['C'])
variant_2 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['G'])
variant_3 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['T'])
variant_4 = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['C'])
variant_1.calls.append(
vcfio.VariantCall(sample_id=hash_name('Sample1'), genotype=[1, 0]))
variant_2.calls.append(
vcfio.VariantCall(sample_id=hash_name('Sample2'), genotype=[1, 0]))
variant_3.calls.append(
vcfio.VariantCall(sample_id=hash_name('Sample3'), genotype=[1, 0]))
variant_4.calls.append(
vcfio.VariantCall(sample_id=hash_name('Sample4'), genotype=[1, 0]))
variants = [variant_1, variant_2, variant_3, variant_4]
merged = vcfio.Variant(reference_name='1',
start=1,
end=2,
reference_bases='A',
alternate_bases=['C'])
merged.calls.append(
vcfio.VariantCall(sample_id=hash_name('Sample1'), genotype=[1, 0]))
merged.calls.append(
vcfio.VariantCall(sample_id=hash_name('Sample4'), genotype=[1, 0]))
merged_variants = list(strategy.get_merged_variants(variants))
self.assertEqual(sorted(merged_variants),
sorted([merged, variant_2, variant_3]))
def _get_variant_merge_strategy(known_args # type: argparse.Namespace
):
# type: (...) -> Optional(variant_merge_strategy.VariantMergeStrategy)
merge_options = variant_transform_options.MergeOptions
if (not known_args.variant_merge_strategy
or known_args.variant_merge_strategy == merge_options.NONE):
return None
elif known_args.variant_merge_strategy == merge_options.MOVE_TO_CALLS:
return move_to_calls_strategy.MoveToCallsStrategy(
known_args.info_keys_to_move_to_calls_regex,
known_args.copy_quality_to_calls, known_args.copy_filter_to_calls)
elif (known_args.variant_merge_strategy ==
merge_options.MERGE_WITH_NON_VARIANTS):
return merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
known_args.info_keys_to_move_to_calls_regex,
known_args.copy_quality_to_calls, known_args.copy_filter_to_calls)
else:
raise ValueError('Merge strategy is not supported.')
def test_merge_mnps(self):
strategy = merge_with_non_variants_strategy.MergeWithNonVariantsStrategy(
None, None, None)
variant_1 = vcfio.Variant(
reference_name='1',
start=5,
end=8,
reference_bases='GTC',
alternate_bases=['G', 'GTCG'],
names=['mnp1', 'mnp2'],
filters=['f1', 'f2'],
quality=1)
variant_2 = vcfio.Variant(
reference_name='1',
start=5,
end=8,
reference_bases='GTC',
alternate_bases=['G', 'GTCG'],
names=['mnp2', 'mnp3'],
filters=['f2', 'f3'],
quality=2)
call_1 = vcfio.VariantCall(name='1', genotype=[1, 2])
call_2 = vcfio.VariantCall(name='2', genotype=[2, 0])
expected = vcfio.Variant(
reference_name='1',
start=5,
end=8,
reference_bases='GTC',
alternate_bases=['G', 'GTCG'],
names=['mnp1', 'mnp2', 'mnp3'],
filters=['f1', 'f2', 'f3'],
quality=2)
expected.calls.append(call_1)
expected.calls.append(call_2)
variant_1.calls.append(call_1)
variant_2.calls.append(call_2)
actual = list(strategy.get_merged_variants([variant_1, variant_2]))
self.assertEqual(actual, [expected])
