def test_sample_ids_combiner_pipeline_preserve_sample_order(self):
sample_ids = [
hash_name('sample2'),
hash_name('sample1'),
hash_name('sample3')
]
variant_calls = [
vcfio.VariantCall(sample_id=sample_ids[0]),
vcfio.VariantCall(sample_id=sample_ids[1]),
vcfio.VariantCall(sample_id=sample_ids[2])
]
variants = [
vcfio.Variant(
calls=[variant_calls[0], variant_calls[1], variant_calls[2]]),
vcfio.Variant(
calls=[variant_calls[0], variant_calls[1], variant_calls[2]])
]
pipeline = TestPipeline()
combined_sample_ids = (
pipeline
| transforms.Create(variants)
| 'CombineSampleIds' >>
combine_sample_ids.SampleIdsCombiner(preserve_sample_order=True)
| combiners.ToList())
assert_that(combined_sample_ids, equal_to([sample_ids]))
pipeline.run()
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 _get_sample_variant_3(file_name='',
use_1_based_coordinate=False,
use_hashing=True):
"""Get third sample variant.
Features:
symbolic alternate
no calls for sample 2
alternate phaseset
"""
hash_name_method = _get_hashing_function(file_name, use_hashing)
variant = vcfio.Variant(reference_name='19',
start=12 if use_1_based_coordinate else 11,
end=12,
reference_bases='C',
alternate_bases=['<SYMBOLIC>'],
quality=49,
filters=['q10'],
info={'AF': [0.5]})
variant.calls.append(
vcfio.VariantCall(sample_id=hash_name_method('Sample1'),
genotype=[0, 1],
phaseset='1',
info={'GQ': 45}))
variant.calls.append(
vcfio.VariantCall(sample_id=hash_name_method('Sample2'),
genotype=[vcfio.MISSING_GENOTYPE_VALUE],
info={'GQ': None}))
return variant
def test_schema_conflict_in_format_field_number(self):
variant = vcfio.Variant(reference_name='chr19',
start=11,
end=12,
reference_bases='CT',
alternate_bases=[],
filters=[],
calls=[
vcfio.VariantCall(name='Sample1',
genotype=[0, 1],
phaseset='*',
info={
'FB': [1, 2],
'FI': [1, 2],
'FSR': 'str'
}),
vcfio.VariantCall(name='Sample2',
genotype=[1, 0],
info={
'FB': [],
'FI': [],
'FSR': ''
})
])
proc_variant = _get_processed_variant(variant)
expected_row = {
ColumnKeyConstants.REFERENCE_NAME:
'chr19',
ColumnKeyConstants.START_POSITION:
11,
ColumnKeyConstants.END_POSITION:
12,
ColumnKeyConstants.REFERENCE_BASES:
'CT',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.CALLS: [
{
ColumnKeyConstants.CALLS_NAME: 'Sample1',
ColumnKeyConstants.CALLS_GENOTYPE: [0, 1],
ColumnKeyConstants.CALLS_PHASESET: '*',
'FB': True,
'FI': 1,
'FSR': ['str']
},
{
ColumnKeyConstants.CALLS_NAME: 'Sample2',
ColumnKeyConstants.CALLS_GENOTYPE: [1, 0],
ColumnKeyConstants.CALLS_PHASESET: None,
'FB': False,
'FI': None,
'FSR': ['']
},
],
}
self.assertEqual(
[expected_row],
list(
self._row_generator.get_rows(proc_variant,
allow_incompatible_records=True)))
def _get_sample_variant_3():
"""Get third sample variant.
Features:
symbolic alternate
no calls for sample 2
alternate phaseset
"""
vcf_line = ('19 12 . C <SYMBOLIC> 49 q10 AF=0.5 GT:PS:GQ 0|1:1:45 '
'.:.:.\n')
variant = vcfio.Variant(
reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['<SYMBOLIC>'],
quality=49,
filters=['q10'],
info={'AF': vcfio.VariantInfo(data=[0.5], field_count='A')})
variant.calls.append(
vcfio.VariantCall(name='Sample1',
genotype=[0, 1],
phaseset='1',
info={'GQ': 45}))
variant.calls.append(
vcfio.VariantCall(name='Sample2',
genotype=[vcfio.MISSING_GENOTYPE_VALUE],
info={'GQ': None}))
return variant, vcf_line
def _get_sample_variants(self):
variant_1 = vcfio.Variant(
reference_name='19', start=11, end=12, reference_bases='C',
alternate_bases=['A', 'TT'], names=['rs1'], quality=2,
filters=['PASS'],
info={'A1': 'some data', 'A2': ['data1', 'data2']},
calls=[
vcfio.VariantCall(
name='Sample1', genotype=[0, 1], phaseset='*',
info={'GQ': 20, 'HQ': [10, 20]}),
vcfio.VariantCall(
name='Sample2', genotype=[1, 0],
info={'GQ': 10, 'FLAG1': True}),
]
)
variant_2 = vcfio.Variant(
reference_name='20', start=11, end=12, reference_bases='C',
alternate_bases=['A', 'TT'], names=['rs1'], quality=20,
filters=['q10'],
info={'A1': 'some data2', 'A3': ['data3', 'data4']},
calls=[
vcfio.VariantCall(name='Sample3', genotype=[1, 1]),
vcfio.VariantCall(
name='Sample4', genotype=[1, 0],
info={'GQ': 20}),
]
)
return [variant_1, variant_2]
def _get_sample_variant_1():
"""Get first sample variant.
Features:
multiple alternates
not phased
multiple names
"""
vcf_line = ('20 1234 rs123;rs2 C A,T 50 PASS AF=0.5,0.1;NS=1 '
'GT:GQ 0/0:48 1/0:20\n')
variant = vcfio.Variant(reference_name='20',
start=1233,
end=1234,
reference_bases='C',
alternate_bases=['A', 'T'],
names=['rs123', 'rs2'],
quality=50,
filters=['PASS'],
info={
'AF':
vcfio.VariantInfo(data=[0.5, 0.1],
field_count='A'),
'NS':
vcfio.VariantInfo(data=1, field_count='1')
})
variant.calls.append(
vcfio.VariantCall(name='Sample1', genotype=[0, 0], info={'GQ': 48}))
variant.calls.append(
vcfio.VariantCall(name='Sample2', genotype=[1, 0], info={'GQ': 20}))
return variant, vcf_line
def _get_sample_variant_2():
"""Get second sample variant.
Features:
multiple references
no alternate
phased
multiple filters
missing format field
"""
vcf_line = ('19 123 rs1234 GTC . 40 q10;s50 NS=2 GT:GQ 1|0:48 0/1:.\n')
variant = vcfio.Variant(
reference_name='19',
start=122,
end=125,
reference_bases='GTC',
alternate_bases=[],
names=['rs1234'],
quality=40,
filters=['q10', 's50'],
info={'NS': vcfio.VariantInfo(data=2, field_count='1')})
variant.calls.append(
vcfio.VariantCall(name='Sample1',
genotype=[1, 0],
phaseset=vcfio.DEFAULT_PHASESET_VALUE,
info={'GQ': 48}))
variant.calls.append(
vcfio.VariantCall(name='Sample2', genotype=[0, 1], info={'GQ': None}))
return variant, vcf_line
def _get_sample_unmerged_variants(self):
# Start/end are different from merged variants.
variant_1 = vcfio.Variant(reference_name='19',
start=123,
end=125,
reference_bases='C',
alternate_bases=['A', 'TT'],
names=['rs2'],
calls=[
vcfio.VariantCall(
sample_id=hash_name('Unmerged1'),
genotype=[0, 1])
])
# Ordering of alternate_bases is different from merged variants.
variant_2 = vcfio.Variant(reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['TT', 'A'],
names=['rs3'],
calls=[
vcfio.VariantCall(
sample_id=hash_name('Unmerged2'),
genotype=[0, 1])
])
return [variant_1, variant_2]
def _get_sample_variant_1(file_name='', use_1_based_coordinate=False,
use_hashing=True, move_hom_ref_calls=False):
"""Get first sample variant.
Features:
multiple alternates
not phased
multiple names
utf-8 encoded
"""
hash_name_method = _get_hashing_function(file_name, use_hashing)
variant = vcfio.Variant(
reference_name='20', start=1233 + use_1_based_coordinate, end=1234,
reference_bases='C', alternate_bases=['A', 'T'], names=['rs123', 'rs2'],
quality=50, filters=['PASS'],
hom_ref_calls=([('Sample1', hash_name_method('Sample1'))] if
move_hom_ref_calls else None),
info={'AF': [0.5, 0.1], 'NS': 1, 'SVTYPE': ['BÑD']})
if not move_hom_ref_calls:
variant.calls.append(
vcfio.VariantCall(sample_id=hash_name_method('Sample1'), name='Sample1',
genotype=[0, 0], info={'GQ': 48}))
variant.calls.append(
vcfio.VariantCall(sample_id=hash_name_method('Sample2'), name='Sample2',
genotype=[1, 0], info={'GQ': 20}))
return variant
def _get_sample_variant(self):
return vcfio.Variant(reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['A', 'TT'],
names=['rs1', 'rs2'],
quality=2,
filters=['PASS'],
info={
'A1': vcfio.VariantInfo('some data', '1'),
'A2': vcfio.VariantInfo(['data1', 'data2'],
'A')
},
calls=[
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
})
])
def _get_sample_variant_2(file_name='', use_1_based_coordinate=False,
use_hashing=True, move_hom_ref_calls=False):
"""Get second sample variant.
Features:
multiple references
no alternate
phased
multiple filters
missing format field
"""
hash_name_method = _get_hashing_function(file_name, use_hashing)
variant = vcfio.Variant(
reference_name='19',
start=122 + use_1_based_coordinate, end=125, reference_bases='GTC',
alternate_bases=[], names=['rs1234'], quality=40,
filters=['q10', 's50'], hom_ref_calls=[] if move_hom_ref_calls else None,
info={'NS': 2})
variant.calls.append(
vcfio.VariantCall(sample_id=hash_name_method('Sample1'), name='Sample1',
genotype=[-1, 0], phaseset=vcfio.DEFAULT_PHASESET_VALUE,
info={'GQ': 48}))
variant.calls.append(
vcfio.VariantCall(sample_id=hash_name_method('Sample2'), name='Sample2',
genotype=[0, -1], info={'GQ': None}))
return variant
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_densify_variants_pipeline(self):
sample_ids = [
hash_name('sample1'),
hash_name('sample2'),
hash_name('sample3')
]
variant_calls = [
vcfio.VariantCall(sample_id=sample_ids[0]),
vcfio.VariantCall(sample_id=sample_ids[1]),
vcfio.VariantCall(sample_id=sample_ids[2]),
]
variants = [
vcfio.Variant(calls=[variant_calls[0], variant_calls[1]]),
vcfio.Variant(calls=[variant_calls[1], variant_calls[2]]),
]
pipeline = TestPipeline()
densified_variants = (
pipeline
| Create(variants)
|
'DensifyVariants' >> densify_variants.DensifyVariants(sample_ids))
assert_that(densified_variants, asserts.has_sample_ids(sample_ids))
pipeline.run()
def test_omit_empty_sample_calls(self):
variant = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='C',
alternate_bases=[], names=['rs1', 'rs2'], quality=2,
filters=['PASS'],
info={},
calls=[
vcfio.VariantCall(
name='Sample1', info={'GQ': None}),
vcfio.VariantCall(
name='Sample2', genotype=[1, 0],
info={'GQ': 10}),
vcfio.VariantCall(
name='Sample3', genotype=[vcfio.MISSING_GENOTYPE_VALUE,
vcfio.MISSING_GENOTYPE_VALUE])])
expected_row = {
ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'C',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.NAMES: ['rs1', 'rs2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS'],
ColumnKeyConstants.CALLS: [
{ColumnKeyConstants.CALLS_NAME: 'Sample2',
ColumnKeyConstants.CALLS_GENOTYPE: [1, 0],
ColumnKeyConstants.CALLS_PHASESET: None,
'GQ': 10}]}
self.assertEqual(
[expected_row],
self._get_row_list_from_variant(variant,
omit_empty_sample_calls=True))
def test_convert_bq_row_to_variant(self):
row = self._get_big_query_row()
expected_variant = vcfio.Variant(reference_name='chr19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['A', 'TT'],
names=['rs1', 'rs2'],
quality=2,
filters=['PASS'],
info={
'IFR': [0.2],
'IFR2': [0.2, 0.3],
'IS': 'some data',
'ISR': ['data1', 'data2']
},
calls=[
vcfio.VariantCall(name='Sample1',
genotype=[0, 1],
phaseset='*',
info={
'GQ': 20,
'FIR':
[10, 20]
}),
vcfio.VariantCall(name='Sample2',
genotype=[1, 0],
info={
'GQ': 10,
'FB': True
})
])
bq_to_variant = bigquery_to_variant.BigQueryToVariant()
self.assertEqual(expected_variant,
bq_to_variant._convert_bq_row_to_variant(row))
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_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 _get_sample_variant_1(is_for_nucleus=False):
"""Get first sample variant.
Features:
multiple alternates
not phased
multiple names
utf-8 encoded
"""
if not is_for_nucleus:
vcf_line = ('20 1234 rs123;rs2 C A,T 50 '
'PASS AF=0.5,0.1;NS=1;SVTYPE=BÑD GT:GQ 0/0:48 1/0:20\n')
variant = vcfio.Variant(reference_name='20',
start=1233,
end=1234,
reference_bases='C',
alternate_bases=['A', 'T'],
names=['rs123', 'rs2'],
quality=50,
filters=['PASS'],
info={
'AF': [0.5, 0.1],
'NS': 1,
'SVTYPE': ['BÑD']
})
variant.calls.append(
vcfio.VariantCall(name='Sample1', genotype=[0, 0], info={'GQ':
48}))
variant.calls.append(
vcfio.VariantCall(name='Sample2', genotype=[1, 0], info={'GQ':
20}))
else:
# 0.1 -> 0.25 float precision loss due to binary floating point conversion.
vcf_line = ('20 1234 rs123;rs2 C A,T 50 '
'PASS AF=0.5,0.25;NS=1 GT:GQ 0/0:48 1/0:20\n')
variant = vcfio.Variant(reference_name='20',
start=1233,
end=1234,
reference_bases='C',
alternate_bases=['A', 'T'],
names=['rs123', 'rs2'],
quality=50,
filters=['PASS'],
info={
'AF': [0.5, 0.25],
'NS': 1
})
variant.calls.append(
vcfio.VariantCall(name='Sample1', genotype=[0, 0], info={'GQ':
48}))
variant.calls.append(
vcfio.VariantCall(name='Sample2', genotype=[1, 0], info={'GQ':
20}))
return variant, vcf_line
def _get_sample_variant_3(is_for_nucleus=False):
"""Get third sample variant.
Features:
symbolic alternate
no calls for sample 2
alternate phaseset
"""
if not is_for_nucleus:
vcf_line = ('19 12 . C <SYMBOLIC> 49 q10 AF=0.5 '
'GT:PS:GQ 0|1:1:45 .:.:.\n')
variant = vcfio.Variant(reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['<SYMBOLIC>'],
quality=49,
filters=['q10'],
info={'AF': [0.5]})
variant.calls.append(
vcfio.VariantCall(name='Sample1',
genotype=[0, 1],
phaseset='1',
info={'GQ': 45}))
variant.calls.append(
vcfio.VariantCall(name='Sample2',
genotype=[vcfio.MISSING_GENOTYPE_VALUE],
info={'GQ': None}))
else:
# '.:.:.' -> './.:.:.' due to Nucleus handeling of VariantCall.genotype.
vcf_line = ('19 12 . C <SYMBOLIC> 49 PASS '
'AF=0.5 GT:PS:GQ 0|1:1:45 ./.:.:.\n')
variant = vcfio.Variant(reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['<SYMBOLIC>'],
quality=49,
filters=['PASS'],
info={'AF': [0.5]})
variant.calls.append(
vcfio.VariantCall(name='Sample1',
genotype=[0, 1],
phaseset='1',
info={'GQ': 45}))
variant.calls.append(
vcfio.VariantCall(name='Sample2',
genotype=[
vcfio.MISSING_GENOTYPE_VALUE,
vcfio.MISSING_GENOTYPE_VALUE
],
info={}))
return variant, vcf_line
def _get_sample_variant_2(is_for_nucleus=False):
"""Get second sample variant.
Features:
multiple references
no alternate
phased
multiple filters
missing format field
"""
if not is_for_nucleus:
vcf_line = ('19 123 rs1234 GTC . 40 q10;s50 NS=2 '
'GT:GQ 1|0:48 0/1:.\n')
variant = vcfio.Variant(reference_name='19',
start=122,
end=125,
reference_bases='GTC',
alternate_bases=[],
names=['rs1234'],
quality=40,
filters=['q10', 's50'],
info={'NS': 2})
variant.calls.append(
vcfio.VariantCall(name='Sample1',
genotype=[1, 0],
phaseset=vcfio.DEFAULT_PHASESET_VALUE,
info={'GQ': 48}))
variant.calls.append(
vcfio.VariantCall(name='Sample2',
genotype=[0, 1],
info={'GQ': None}))
else:
# 'q10;s50' -> 'PASS' due to missing header fields.
vcf_line = ('19 123 rs1234 GTC . 40 PASS NS=2 ' 'GT:GQ 1|0:48 0/1:.\n')
variant = vcfio.Variant(reference_name='19',
start=122,
end=125,
reference_bases='GTC',
alternate_bases=[],
names=['rs1234'],
quality=40,
filters=['PASS'],
info={'NS': 2})
variant.calls.append(
vcfio.VariantCall(name='Sample1',
genotype=[1, 0],
phaseset=vcfio.DEFAULT_PHASESET_VALUE,
info={'GQ': 48}))
variant.calls.append(
vcfio.VariantCall(name='Sample2', genotype=[0, 1], info={}))
return variant, vcf_line
def test_all_fields(self):
variant = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='C',
alternate_bases=['A', 'TT'], names=['rs1', 'rs2'], quality=2,
filters=['PASS'],
info={'IFR': [0.1, 0.2],
'IFR2': [0.2, 0.3],
'IS': 'some data',
'ISR': ['data1', 'data2']},
calls=[
vcfio.VariantCall(
name='Sample1', genotype=[0, 1], phaseset='*',
info={'GQ': 20, 'FIR': [10, 20]}),
vcfio.VariantCall(
name='Sample2', genotype=[1, 0],
info={'GQ': 10, 'FB': True}),
vcfio.VariantCall(
name='Sample3', genotype=[vcfio.MISSING_GENOTYPE_VALUE])])
header_num_dict = {'IFR': 'A', 'IFR2': 'A', 'IS': '1', 'ISR': '2'}
expected_row = {
ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'C',
ColumnKeyConstants.ALTERNATE_BASES: [
{ColumnKeyConstants.ALTERNATE_BASES_ALT: 'A',
'IFR': 0.1, 'IFR2': 0.2},
{ColumnKeyConstants.ALTERNATE_BASES_ALT: 'TT',
'IFR': 0.2, 'IFR2': 0.3}],
ColumnKeyConstants.NAMES: ['rs1', 'rs2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS'],
ColumnKeyConstants.CALLS: [
{ColumnKeyConstants.CALLS_NAME: 'Sample1',
ColumnKeyConstants.CALLS_GENOTYPE: [0, 1],
ColumnKeyConstants.CALLS_PHASESET: '*',
'GQ': 20, 'FIR': [10, 20]},
{ColumnKeyConstants.CALLS_NAME: 'Sample2',
ColumnKeyConstants.CALLS_GENOTYPE: [1, 0],
ColumnKeyConstants.CALLS_PHASESET: None,
'GQ': 10, 'FB': True},
{ColumnKeyConstants.CALLS_NAME: 'Sample3',
ColumnKeyConstants.CALLS_GENOTYPE: [vcfio.MISSING_GENOTYPE_VALUE],
ColumnKeyConstants.CALLS_PHASESET: None}],
'IS': 'some data',
'ISR': ['data1', 'data2']}
self.assertEqual([expected_row],
self._get_row_list_from_variant(variant, header_num_dict))
def _get_sample_variant_1(self, split_alternate_allele_info_fields=True):
variant = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='C',
alternate_bases=['A', 'TT'], names=['rs1', 'rs2'], quality=2,
filters=['PASS'],
info={'IFR': [0.1, 0.2], 'IFR2': [0.2, 0.3],
'IS': 'some data', 'ISR': ['data1', 'data2']},
calls=[
vcfio.VariantCall(
sample_id=hash_name('Sample1'), genotype=[0, 1], phaseset='*',
info={'GQ': 20, 'FIR': [10, 20]}),
vcfio.VariantCall(
sample_id=hash_name('Sample2'), genotype=[1, 0],
info={'GQ': 10, 'FB': True}),
]
)
header_num_dict = {'IFR': 'A', 'IFR2': 'A', 'IS': '1', 'ISR': '2'}
row = {ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'C',
ColumnKeyConstants.NAMES: ['rs1', 'rs2'],
ColumnKeyConstants.QUALITY: 2,
ColumnKeyConstants.FILTER: ['PASS'],
ColumnKeyConstants.CALLS: [
{ColumnKeyConstants.CALLS_SAMPLE_ID: hash_name('Sample1'),
ColumnKeyConstants.CALLS_GENOTYPE: [0, 1],
ColumnKeyConstants.CALLS_PHASESET: '*',
'GQ': 20, 'FIR': [10, 20]},
{ColumnKeyConstants.CALLS_SAMPLE_ID: hash_name('Sample2'),
ColumnKeyConstants.CALLS_GENOTYPE: [1, 0],
ColumnKeyConstants.CALLS_PHASESET: None,
'GQ': 10, 'FB': True}],
'IS': 'some data',
'ISR': ['data1', 'data2']}
if split_alternate_allele_info_fields:
row[ColumnKeyConstants.ALTERNATE_BASES] = [
{ColumnKeyConstants.ALTERNATE_BASES_ALT:
'A', 'IFR': 0.1, 'IFR2': 0.2},
{ColumnKeyConstants.ALTERNATE_BASES_ALT:
'TT', 'IFR': 0.2, 'IFR2': 0.3}]
else:
row[ColumnKeyConstants.ALTERNATE_BASES] = [
{ColumnKeyConstants.ALTERNATE_BASES_ALT: 'A'},
{ColumnKeyConstants.ALTERNATE_BASES_ALT: 'TT'}]
row['IFR'] = [0.1, 0.2]
row['IFR2'] = [0.2, 0.3]
return variant, row, header_num_dict
def _get_sample_variant_with_empty_calls(self):
variant = vcfio.Variant(reference_name='20',
start=123,
end=125,
reference_bases='CT',
alternate_bases=[],
filters=['q10', 's10'],
info={'II': 1234},
calls=[
vcfio.VariantCall(name='EmptySample',
genotype=[],
phaseset='*',
info={}),
])
header_num_dict = {'II': '1'}
row = {
ColumnKeyConstants.REFERENCE_NAME: '20',
ColumnKeyConstants.START_POSITION: 123,
ColumnKeyConstants.END_POSITION: 125,
ColumnKeyConstants.REFERENCE_BASES: 'CT',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.FILTER: ['q10', 's10'],
ColumnKeyConstants.CALLS: [],
'II': 1234
}
return variant, row, header_num_dict
def _densify_variants(self, variant, all_call_names):
# type: (vcf_parser.Variant, List[str]) -> vcf_parser.Variant
"""Cherry-picks calls for the variant.
The calls are in the same order as the `all_call_names`.
Args:
variant: The variant that will be modified to contain calls for
`all_call_names`.
all_call_names: A list of sample names that used to cherry-pick each
variant'calls. If one call is missing, an empty `VariantCall` is added.
Returns:
`variant` modified to contain calls for `all_call_names`.
"""
existing_call_name = {call.name: call for call in variant.calls}
new_calls = []
for call_name in all_call_names:
if call_name in existing_call_name.keys():
new_calls.append(existing_call_name.get(call_name))
else:
new_calls.append(
vcfio.VariantCall(name=call_name,
genotype=vcfio.MISSING_GENOTYPE_VALUE))
variant.calls = new_calls
return variant
def _get_sample_variant_with_incompatible_records(self):
variant = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='C',
alternate_bases=[], filters=['PASS'],
info={'IFR': ['0.1', '0.2'], 'IS': 1, 'ISR': 1},
calls=[
vcfio.VariantCall(
sample_id=hash_name('Sample1'), genotype=[0, 1], phaseset='*',
info={'GQ': 20, 'FIR': [10.0, 20.0]}),
]
)
header_num_dict = {'IFR': '2', 'IS': '1', 'ISR': '1'}
row = {ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'C',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.FILTER: ['PASS'],
ColumnKeyConstants.CALLS: [
{ColumnKeyConstants.CALLS_SAMPLE_ID: hash_name('Sample1'),
ColumnKeyConstants.CALLS_GENOTYPE: [0, 1],
ColumnKeyConstants.CALLS_PHASESET: '*',
'GQ': 20, 'FIR': [10, 20]}],
'IFR': [0.1, 0.2],
'IS': '1',
'ISR': ['1']}
return variant, row, header_num_dict
def test_add_missing_calls(self):
transform = densify_variants.DensifyVariants()
variant = vcfio.Variant(calls=[vcfio.VariantCall(name='sample2')])
new_variant = transform._densify_variants(
variant, ['sample1', 'sample2', 'sample3'])
call_names = [call.name for call in new_variant.calls]
self.assertItemsEqual(call_names, ['sample1', 'sample2', 'sample3'])
def _get_sample_variant_1(self):
variant = vcfio.Variant(reference_name='chr19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['A', 'TT'],
names=['rs1', 'rs2'],
quality=2,
filters=['PASS'],
info={
'IS': 'some data',
'ISI': '1',
'ISF': '1.0',
'IF': 1.0,
'IB': True,
'IA': [1, 2]
},
calls=[
vcfio.VariantCall(
sample_id=hash_name('Sample1'),
genotype=[0, 1],
phaseset='*',
info={
'FI': 20,
'FU': [10.0, 20.0]
})
])
return variant
