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)