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_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']
})
variant_2 = vcfio.Variant(reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['A', 'TT'],
names=['rs1'],
quality=20,
filters=['q10'],
info={
'A1': 'some data2',
'A3': ['data3', 'data4']
})
return [variant_1, variant_2]
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 _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_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 test_schema_conflict_in_info_field_type(self):
variant = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='CT',
alternate_bases=[], filters=[],
info={'IB': 1,
'II': 1.1,
'IFR': [1, 2],
'ISR': [1.0, 2.0]})
header_num_dict = {'IB': '1', 'II': '1', 'IFR': '2', 'ISR': '2'}
expected_row = {
ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'CT',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.CALLS: [],
'IB': True,
'II': 1,
'IFR': [1.0, 2.0],
'ISR': ['1.0', '2.0']}
self.assertEqual([expected_row], self._get_row_list_from_variant(
variant, header_num_dict, allow_incompatible_records=True))
with self.assertRaises(ValueError):
variant = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='CT',
alternate_bases=[], filters=[],
# String cannot be casted to integer.
info={'II': '1.1'})
header_num_dict = {'II': '1'}
self._get_row_list_from_variant(
variant, header_num_dict, allow_incompatible_records=True)
self.fail('String data for an integer schema must cause an exception')
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_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_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_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 _get_sample_variants(self):
variant1 = vcfio.Variant(
reference_name='chr19', start=11, end=12, reference_bases='C')
variant2 = vcfio.Variant(
reference_name='20', start=123, end=125, reference_bases='CT')
variant3 = vcfio.Variant(
reference_name='20', start=None, end=None, reference_bases=None)
variant4 = vcfio.Variant(
reference_name='20', start=123, end=125, reference_bases='CT')
return [variant1, variant2, variant3, variant4]
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_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_nonstandard_float_values(self):
variant = vcfio.Variant(
reference_name='chr19',
start=11,
end=12,
reference_bases='CT',
alternate_bases=[],
filters=[],
info={
'F1': vcfio.VariantInfo(float('inf'), '1'),
'F2': vcfio.VariantInfo(
[float('-inf'), float('nan'), 1.2], '3'),
'F3': vcfio.VariantInfo(float('nan'), '1'),
})
null_replacement_value = -sys.maxint
expected_row = {
ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'CT',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.CALLS: [],
'F1': sys.maxint,
'F2': [-sys.maxint, null_replacement_value, 1.2],
'F3': None
}
self.assertEqual([expected_row],
self._get_row_list_from_variant(variant))
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 _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_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_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_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
def test_unicode_fields(self):
sample_unicode_str = u'\xc3\xb6'
sample_utf8_str = sample_unicode_str.encode('utf-8')
variant = vcfio.Variant(reference_name='chr19',
start=11,
end=12,
reference_bases='CT',
alternate_bases=[],
filters=[sample_unicode_str, sample_utf8_str],
info={
'IS': sample_utf8_str,
'ISR':
[sample_unicode_str, sample_utf8_str]
})
header_num_dict = {'IS': '1', 'ISR': '2'}
proc_variant = _get_processed_variant(variant, header_num_dict)
expected_row = {
ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'CT',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.FILTER:
[sample_unicode_str, sample_unicode_str],
ColumnKeyConstants.CALLS: [],
'IS': sample_unicode_str,
'ISR': [sample_unicode_str, sample_unicode_str]
}
self.assertEqual([expected_row],
list(self._row_generator.get_rows(proc_variant)))
def test_no_alternate_bases(self):
variant = vcfio.Variant(reference_name='chr19',
start=11,
end=12,
reference_bases='CT',
alternate_bases=[],
filters=['q10'],
info={
'IS': 'some data',
'ISR': ['data1', 'data2']
})
header_num_dict = {'IS': '1', 'ISR': '2'}
proc_variant = _get_processed_variant(variant, header_num_dict)
expected_row = {
ColumnKeyConstants.REFERENCE_NAME: 'chr19',
ColumnKeyConstants.START_POSITION: 11,
ColumnKeyConstants.END_POSITION: 12,
ColumnKeyConstants.REFERENCE_BASES: 'CT',
ColumnKeyConstants.ALTERNATE_BASES: [],
ColumnKeyConstants.FILTER: ['q10'],
ColumnKeyConstants.CALLS: [],
'IS': 'some data',
'ISR': ['data1', 'data2']
}
self.assertEqual([expected_row],
list(self._row_generator.get_rows(proc_variant)))
def test_create_processed_variant_annotation_alt_prefix(self):
# The returned variant is ignored as we create a custom one next.
_, header_fields = self._get_sample_variant_and_header_with_csq()
variant = vcfio.Variant(
reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['CT', 'CC', 'CCC'],
names=['rs1'],
quality=2,
filters=['PASS'],
info={'CSQ': ['T|C1|I1|S1|G1', 'C|C2|I2|S2|G2', 'CC|C3|I3|S3|G3']})
counter_factory = _CounterSpyFactory()
factory = processed_variant.ProcessedVariantFactory(
header_fields,
split_alternate_allele_info_fields=True,
annotation_fields=['CSQ'],
counter_factory=counter_factory)
proc_var = factory.create_processed_variant(variant)
alt1 = processed_variant.AlternateBaseData('CT')
alt1._info = {
'CSQ': [{
annotation_parser.ANNOTATION_ALT: 'T',
'Consequence': 'C1',
'IMPACT': 'I1',
'SYMBOL': 'S1',
'Gene': 'G1'
}]
}
alt2 = processed_variant.AlternateBaseData('CC')
alt2._info = {
'CSQ': [{
annotation_parser.ANNOTATION_ALT: 'C',
'Consequence': 'C2',
'IMPACT': 'I2',
'SYMBOL': 'S2',
'Gene': 'G2'
}]
}
alt3 = processed_variant.AlternateBaseData('CCC')
alt3._info = {
'CSQ': [{
annotation_parser.ANNOTATION_ALT: 'CC',
'Consequence': 'C3',
'IMPACT': 'I3',
'SYMBOL': 'S3',
'Gene': 'G3'
}]
}
self.assertEqual(proc_var.alternate_data_list, [alt1, alt2, alt3])
self.assertFalse(proc_var.non_alt_info.has_key('CSQ'))
self.assertEqual(
counter_factory.counter_map[CEnum.VARIANT.value].get_value(), 1)
self.assertEqual(
counter_factory.counter_map[
CEnum.ANNOTATION_ALT_MATCH.value].get_value(), 3)
self.assertEqual(
counter_factory.counter_map[
CEnum.ANNOTATION_ALT_MISMATCH.value].get_value(), 0)
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_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 _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 test_get_merge_keys(self):
strategy = move_to_calls_strategy.MoveToCallsStrategy(None, None, None)
def get_expected_key(reference_name, start, end, reference_bases,
alternate_bases):
return '%s:%s:%s:%s:%s' % (
reference_name or '', str(start or ''), str(
end or ''), strategy._get_hash(reference_bases or ''),
strategy._get_hash(','.join(alternate_bases or [])))
variant = vcfio.Variant()
self.assertEqual(get_expected_key(None, None, None, None, None),
next(strategy.get_merge_keys(variant)))
variant.reference_name = '19'
self.assertEqual(get_expected_key(19, None, None, None, None),
next(strategy.get_merge_keys(variant)))
variant.start = 123
variant.end = 125
variant.reference_bases = 'AT'
self.assertEqual(get_expected_key(19, 123, 125, 'AT', None),
next(strategy.get_merge_keys(variant)))
variant.alternate_bases = ['A', 'C']
self.assertEqual(get_expected_key(19, 123, 125, 'AT', ['A', 'C']),
next(strategy.get_merge_keys(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)))
