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"""Tests for variantcall_utils."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import functools
from absl.testing import absltest
from absl.testing import parameterized
import mock
from third_party.nucleus.protos import struct_pb2
from third_party.nucleus.protos import variants_pb2
from third_party.nucleus.util import struct_utils
from third_party.nucleus.util import variantcall_utils
class VariantcallUtilsTests(parameterized.TestCase):
def _assert_struct_lists_equal(self, actual, expected):
self.assertEqual(len(actual), len(expected))
for actual_elem, expected_elem in zip(actual, expected):
self.assertEqual(actual_elem, expected_elem)
@parameterized.parameters(
dict(
field_name='GP',
value=[.1, .2, .7],
reader=None,
expected=[struct_pb2.Value(number_value=v) for v in [.1, .2, .7]]),
dict(
field_name='AD',
value=[23],
reader=None,
expected=[struct_pb2.Value(int_value=23)]),
dict(
field_name='FT',
value=['PASS'],
reader=None,
expected=[struct_pb2.Value(string_value='PASS')]),
dict(
field_name='FT',
value=['PASS'],
reader=True,
expected=[struct_pb2.Value(string_value='PASS')]),
)
def test_set_format(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_set_fn.return_value = (
struct_utils.set_string_field)
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, field_name, value, reader)
actual = call.info[field_name].values
self._assert_struct_lists_equal(actual, expected)
@parameterized.parameters(
dict(field_name='GP', reader=None, expected=[.1, .2, .7]),
dict(field_name='AD', reader=None, expected=[55, 3]),
dict(field_name='DP', reader=None, expected=58),
dict(field_name='GL', reader=None, expected=[-1, -3, -5.5]),
dict(field_name='GT', reader=None, expected=[0, 1]),
dict(field_name='FT', reader=None, expected='LowQual'),
dict(field_name='FT', reader=True, expected='LowQual'),
)
def test_get_format(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_get_fn.return_value = (
functools.partial(
struct_utils.get_string_field, is_single_field=True))
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, 'GP', [.1, .2, .7])
variantcall_utils.set_format(call, 'AD', [55, 3])
variantcall_utils.set_format(call, 'DP', 58)
variantcall_utils.set_format(call, 'GL', [-1, -3, -5.5])
variantcall_utils.set_format(call, 'GT', [0, 1])
variantcall_utils.set_format(call, 'FT', ['LowQual'])
actual = variantcall_utils.get_format(call, field_name, vcf_object=reader)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(
field_name='AD',
setter=variantcall_utils.set_ad,
getter=variantcall_utils.get_ad,
values=[[1, 5], [30, 29]]),
dict(
field_name='GL',
setter=variantcall_utils.set_gl,
getter=variantcall_utils.get_gl,
values=[[-1, -2, -3.3], [-0.001, -3, -10]]),
dict(
field_name='GQ',
setter=variantcall_utils.set_gq,
getter=variantcall_utils.get_gq,
values=range(10)),
dict(
field_name='GT',
setter=variantcall_utils.set_gt,
getter=variantcall_utils.get_gt,
values=[[0, 1], [1, 1], [1, 2]]),
dict(
field_name='MIN_DP',
setter=variantcall_utils.set_min_dp,
getter=variantcall_utils.get_min_dp,
values=range(10)),
dict(
field_name='MED_DP',
setter=variantcall_utils.set_med_dp,
getter=variantcall_utils.get_med_dp,
values=range(10)),
)
def test_variantcall_format_roundtrip(self, field_name, setter, getter,
values):
vc = variants_pb2.VariantCall()
self.assertNotIn(field_name, vc.info)
for value in values:
setter(vc, value)
if field_name not in ['GT', 'GL']:
self.assertIn(field_name, vc.info)
actual = getter(vc)
self.assertEqual(actual, value)
@parameterized.parameters(
dict(genotype=[], expected=False),
dict(genotype=[-1], expected=False),
dict(genotype=[-1, -1], expected=False),
dict(genotype=[-1, -1073741825], expected=False),
dict(genotype=[-1, 0], expected=True),
dict(genotype=[0, 0], expected=True),
dict(genotype=[0, 1], expected=True),
dict(genotype=[0, 1, -1], expected=True),
dict(genotype=[-1, 0, -1073741825], expected=True),
)
def test_has_genotypes(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.has_genotypes(call)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(genotype=[], expected=True),
dict(genotype=[-1], expected=False),
dict(genotype=[-1, -1073741825], expected=False),
dict(genotype=[-1, 0], expected=False),
dict(genotype=[0, 0], expected=True),
dict(genotype=[0, 1], expected=True),
dict(genotype=[0, 1, -1], expected=False),
dict(genotype=[1, 0, -1073741825], expected=False),
)
def test_has_full_genotypes(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.has_full_genotypes(call)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(genotype=[], expected=0),
dict(genotype=[-1], expected=1),
dict(genotype=[-1, -1], expected=2),
dict(genotype=[-1, -1073741825], expected=1),
dict(genotype=[-1, 0], expected=2),
dict(genotype=[0, 0], expected=2),
dict(genotype=[0, 1], expected=2),
dict(genotype=[0, 1, -1], expected=3),
dict(genotype=[-1, 0, -1073741825], expected=2),
)
def test_ploidy(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.ploidy(call)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(genotype=[], expected=False),
dict(genotype=[-1], expected=False),
dict(genotype=[-1, -1], expected=False),
dict(genotype=[-1, -1073741825], expected=False),
dict(genotype=[-1, 0], expected=False),
dict(genotype=[0, 0], expected=False),
dict(genotype=[0, 1], expected=True),
dict(genotype=[0, 1, -1], expected=True),
dict(genotype=[-1, 0, -1073741825], expected=False),
)
def test_has_variation(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.has_variation(call)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(genotype=[], expected=False),
dict(genotype=[-1], expected=False),
dict(genotype=[-1, -1], expected=False),
dict(genotype=[-1, -1073741825], expected=False),
dict(genotype=[-1, 0], expected=False),
dict(genotype=[0, 0], expected=False),
dict(genotype=[0, 1], expected=True),
dict(genotype=[0, 2], expected=True),
dict(genotype=[1, 1], expected=False),
dict(genotype=[2, 2], expected=False),
dict(genotype=[1, 2], expected=True),
dict(genotype=[0, 1, -1], expected=True),
dict(genotype=[0, 1, 2], expected=True),
dict(genotype=[-1, 0, -1073741825], expected=False),
)
def test_is_heterozygous(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.is_heterozygous(call)
self.assertEqual(actual, expected)
if __name__ == '__main__':
absltest.main()
