def test_set_info(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_set_fn.return_value = (
struct_utils.set_string_field)
variant = variants_pb2.Variant()
variant_utils.set_info(variant, field_name, value, reader)
actual = variant.info[field_name].values
self.assertEqual(len(actual), len(expected))
for actual_elem, expected_elem in zip(actual, expected):
self.assertEqual(actual_elem, expected_elem)
def test_set_info(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_set_fn.return_value = (
struct_utils.set_string_field)
variant = variants_pb2.Variant()
variant_utils.set_info(variant, field_name, value, reader)
actual = variant.info[field_name].values
self.assertEqual(len(actual), len(expected))
for actual_elem, expected_elem in zip(actual, expected):
self.assertEqual(actual_elem, expected_elem)
def _add_class_to_variant(variant, class_status):
if class_status is None:
return variant
header = variants_pb2.VcfHeader(
infos=[
variants_pb2.VcfInfo(
id=CUSTOMIZED_INFO_FIELD_NAME,
number='A',
type=vcf_constants.STRING_TYPE,
description='Customized class label for the variant.')])
my_cache = vcf.VcfHeaderCache(header)
vcf_object = FakeVCFObject(field_access_cache=my_cache)
variant_utils.set_info(variant, CUSTOMIZED_INFO_FIELD_NAME, class_status,
vcf_object=vcf_object)
return variant
def test_get_info(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_get_fn.return_value = (
functools.partial(
struct_utils.get_string_field, is_single_field=True))
variant = variants_pb2.Variant()
variant_utils.set_info(variant, 'AD', [23, 25])
variant_utils.set_info(variant, 'AA', 'C')
variant_utils.set_info(variant, '1000G', True)
variant_utils.set_info(variant, 'DB', False)
actual = variant_utils.get_info(variant, field_name, vcf_object=reader)
self.assertEqual(actual, expected)
def test_get_info(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_get_fn.return_value = (
functools.partial(
struct_utils.get_string_field, is_single_field=True))
variant = variants_pb2.Variant()
variant_utils.set_info(variant, 'AD', [23, 25])
variant_utils.set_info(variant, 'AA', 'C')
variant_utils.set_info(variant, '1000G', True)
variant_utils.set_info(variant, 'DB', False)
actual = variant_utils.get_info(variant, field_name, vcf_object=reader)
self.assertEqual(actual, expected)
