def test_get_annotation_names(self):
schema_with_annotations = bigquery_schema_util.get_sample_table_schema(
with_annotation_fields=True)
self.assertEqual(
bq_to_vcf._extract_annotation_names(schema_with_annotations),
{'CSQ': ['Consequence', 'IMPACT']})
schema_with_no_annotation = bigquery_schema_util.get_sample_table_schema(
)
self.assertEqual(
bq_to_vcf._extract_annotation_names(schema_with_no_annotation), {})
def test_schema_to_vcf_header_to_schema(self):
original_schema = bigquery_schema_util.get_sample_table_schema()
header = bigquery_vcf_schema_converter.generate_header_fields_from_schema(
original_schema)
reconstructed_schema = (
bigquery_vcf_schema_converter.generate_schema_from_header_fields(
header, processed_variant.ProcessedVariantFactory(header)))
self.assertEqual(_get_fields_from_schema(reconstructed_schema),
_get_fields_from_schema(original_schema))
def test_generate_header_fields_from_schema(self):
sample_schema = bigquery_schema_util.get_sample_table_schema()
header = schema_converter.generate_header_fields_from_schema(
sample_schema)
infos = OrderedDict([
('AF', createInfo('AF', 'A', 'Float', 'desc', None, None)),
('AA', createInfo('AA', 1, 'String', 'desc', None, None)),
('IFR', createInfo('IFR', '.', 'Float', 'desc', None, None)),
('IS', createInfo('IS', 1, 'String', 'desc', None, None))])
formats = OrderedDict([
('FB', createFormat('FB', 1, 'String', 'desc')),
('GQ', createFormat('GQ', 1, 'Integer', 'desc'))])
expected_header = vcf_header_io.VcfHeader(infos=infos, formats=formats)
self.assertEqual(header, expected_header)
def test_generate_header_fields_from_schema_with_annotation(self):
sample_schema = bigquery_schema_util.get_sample_table_schema(
with_annotation_fields=True)
header = bigquery_vcf_schema_converter.generate_header_fields_from_schema(
sample_schema)
infos = OrderedDict([
('AF', Info('AF', field_counts['A'], 'Float', 'desc', None, None)),
('CSQ',
Info('CSQ', field_counts['.'], 'String',
'desc Format: Consequence|IMPACT', None, None)),
('AA', Info('AA', 1, 'String', 'desc', None, None)),
('IFR', Info('IFR', field_counts['.'], 'Float', 'desc', None,
None)),
('IS', Info('IS', 1, 'String', 'desc', None, None))
])
formats = OrderedDict([('FB', parser._Format('FB', 0, 'Flag', 'desc')),
('GQ', parser._Format('GQ', 1, 'Integer',
'desc'))])
expected_header = vcf_header_io.VcfHeader(infos=infos, formats=formats)
self.assertEqual(header, expected_header)
