def test_infer_annotation_types_with_multiple_annotation_fields(self):
anno_fields = ['CSQ', 'CSQ_VT']
infos = self._get_annotation_infos()
infos['CSQ_VT'] = createInfo(
'CSQ_VT', 'A', 'String',
'Annotations from VEP. Format: Allele|Gene|Position|Score',
'source', 'v')
variant = self._get_sample_variant_1()
variant.info['CSQ_VT'] = ['A|1|100|1.2', 'A|2|101|1.3']
variant.info['CSQ'] = ['A|1|100|1.2', 'A|2|101|1.3']
inferred_infos = infer_headers_util.infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos), False, anno_fields)
expected_infos = {
'CSQ_Gene_TYPE':
self._get_inferred_info('CSQ', 'Gene', 'Integer'),
'CSQ_Position_TYPE':
self._get_inferred_info('CSQ', 'Position', 'Integer'),
'CSQ_Score_TYPE':
self._get_inferred_info('CSQ', 'Score', 'Float'),
'CSQ_VT_Gene_TYPE':
self._get_inferred_info('CSQ_VT', 'Gene', 'Integer'),
'CSQ_VT_Position_TYPE':
self._get_inferred_info('CSQ_VT', 'Position', 'Integer'),
'CSQ_VT_Score_TYPE':
self._get_inferred_info('CSQ_VT', 'Score', 'Float')
}
self.assertDictEqual(expected_infos, inferred_infos)
def test_infer_annotation_empty_info(self):
anno_fields = ['CSQ']
infos = self._get_annotation_infos()
variant = self._get_sample_variant_1()
variant.info['CSQ'] = []
inferred_infos = infer_headers_util.infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos), False, anno_fields)
self.assertEqual({}, inferred_infos)
def test_infer_info_fields_no_conflicts(self):
variant = self._get_sample_variant_1()
infos = {
'IS': createInfo('IS', 1, 'String', ''),
'ISI': createInfo('ISI', 1, 'Integer', ''),
'ISF': createInfo('ISF', 1, 'Float', ''),
'IF': createInfo('IF', 1, 'Float', ''),
'IB': createInfo('IB', 0, 'Flag', ''),
'IA': createInfo('IA', 'A', 'Float', '')
}
inferred_infos = infer_headers_util.infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos), infer_headers=True)
self.assertEqual({}, inferred_infos)
def test_infer_annotation_types_with_missing(self):
anno_fields = ['CSQ']
infos = self._get_annotation_infos()
variant = self._get_sample_variant_1()
variant.info['CSQ'] = ['A||100|', 'A||101|1.3', 'A|||1.4', 'TT|||']
inferred_infos = infer_headers_util.infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos), False, anno_fields)
expected_infos = {
'CSQ_Gene_TYPE':
self._get_inferred_info('CSQ', 'Gene', '.'),
'CSQ_Position_TYPE':
self._get_inferred_info('CSQ', 'Position', 'Integer'),
'CSQ_Score_TYPE':
self._get_inferred_info('CSQ', 'Score', 'Float')
}
self.assertDictEqual(expected_infos, inferred_infos)
def test_infer_annotation_types_no_conflicts(self):
anno_fields = ['CSQ']
infos = self._get_annotation_infos()
variant = self._get_sample_variant_1()
variant.info['CSQ'] = ['A|GENE1|100|1.2', 'TT|GENE1|101|1.3']
inferred_infos = infer_headers_util.infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos), True, anno_fields)
expected_infos = {
'CSQ_Gene_TYPE':
self._get_inferred_info('CSQ', 'Gene', 'String'),
'CSQ_Position_TYPE':
self._get_inferred_info('CSQ', 'Position', 'Integer'),
'CSQ_Score_TYPE':
self._get_inferred_info('CSQ', 'Score', 'Float')
}
self.assertDictEqual(expected_infos, inferred_infos)
def test_infer_info_fields_combined_conflicts(self):
variant = self._get_sample_variant_info_ia_cardinality_mismatch()
infos = {
'IS': createInfo('IS', 1, 'String', ''),
'ISI': createInfo('ISI', 1, 'Integer', ''),
'ISF': createInfo('ISF', 1, 'Float', ''),
'IB': createInfo('IB', 0, 'Flag', ''),
'IA': createInfo('IA', 'A', 'Integer', '')
}
inferred_infos = infer_headers_util.infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos), infer_headers=True)
expected_infos = {
'IF': createInfo('IF', 1, 'Float', ''),
'IA': createInfo('IA', '.', 'Float', '')
}
self.assertEqual(expected_infos, inferred_infos)
def process(self,
variant, # type: vcfio.Variant
defined_headers # type: vcf_header_io.VcfHeader
):
# type: (...) -> Iterable[vcf_header_io.VcfHeader]
"""
Args:
defined_headers: header fields defined in header section of VCF files.
"""
infos = infer_headers_util.infer_info_fields(
variant,
defined_headers,
self._infer_headers,
self._annotation_fields_to_infer)
formats = {}
if self._infer_headers:
formats = infer_headers_util.infer_format_fields(variant, defined_headers)
yield vcf_header_io.VcfHeader(infos=infos, formats=formats)
