def test_infer_annotation_types_with_multiple_annotation_fields(self):
anno_fields = ['CSQ', 'CSQ_VT']
csq_vt = [
('CSQ_VT',
createInfo(
'CSQ_VT', 'A', 'String',
'Annotations from VEP. Format: Allele|Gene|Position|Score',
'source', 'v'))
]
header = self._get_sample_header_fields(with_annotation=csq_vt)
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']
infer_header_fields = infer_headers._InferHeaderFields(
False, anno_fields)
inferred_headers = next(infer_header_fields.process(variant, header))
expected_types = {
'CSQ_Gene_TYPE': 'Integer',
'CSQ_Position_TYPE': 'Integer',
'CSQ_Score_TYPE': 'Float',
'CSQ_VT_Gene_TYPE': 'Integer',
'CSQ_VT_Position_TYPE': 'Integer',
'CSQ_VT_Score_TYPE': 'Float'
}
for key, item in inferred_headers.infos.items():
self.assertEqual(item['type'], expected_types[key])
self.assertEqual(len(expected_types), len(inferred_headers.infos))
def test_infer_format_fields_no_conflicts(self):
variant = self._get_sample_variant_1()
formats = OrderedDict([
('FS', Format('FS', 1, 'String', 'desc')),
('FI', Format('FI', 2, 'Integer', 'desc')),
('FU', Format('FU', field_counts['.'], 'Float', 'desc')),
('GT', Format('GT', 2, 'Integer', 'Special GT key')),
('PS', Format('PS', 1, 'Integer', 'Special PS key'))])
infer_header_fields = infer_headers._InferHeaderFields()
header = infer_header_fields._infer_format_fields(
variant, vcf_header_io.VcfHeader(formats=formats))
self.assertEqual({}, header)
def test_infer_info_fields_no_conflicts(self):
variant = self._get_sample_variant_1()
infos = {'IS': Info('IS', 1, 'String', '', '', ''),
'ISI': Info('ISI', 1, 'Integer', '', '', ''),
'ISF': Info('ISF', 1, 'Float', '', '', ''),
'IF': Info('IF', 1, 'Float', '', '', ''),
'IB': Info('IB', 0, 'Flag', '', '', ''),
'IA': Info('IA', -1, 'Float', '', '', '')}
infer_header_fields = infer_headers._InferHeaderFields()
inferred_infos = infer_header_fields._infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos))
self.assertEqual({}, inferred_infos)
def test_infer_format_fields_combined_conflicts(self):
variant = self._get_sample_variant_format_fi_float_value()
formats = OrderedDict([
('FS', Format('FS', 1, 'String', 'desc')),
('FI', Format('FI', 2, 'Integer', 'desc')),
('GT', Format('GT', 2, 'Integer', 'Special GT key')),
('PS', Format('PS', 1, 'Integer', 'Special PS key'))])
infer_header_fields = infer_headers._InferHeaderFields()
inferred_formats = infer_header_fields._infer_format_fields(
variant, vcf_header_io.VcfHeader(formats=formats))
expected_formats = {'FI': Format('FI', 2, 'Float', 'desc'),
'FU': Format('FU', field_counts['.'], 'Float', '')}
self.assertEqual(expected_formats, inferred_formats)
def test_infer_info_fields_combined_conflicts(self):
variant = self._get_sample_variant_info_ia_cardinality_mismatch()
infos = {'IS': Info('IS', 1, 'String', '', '', ''),
'ISI': Info('ISI', 1, 'Integer', '', '', ''),
'ISF': Info('ISF', 1, 'Float', '', '', ''),
'IB': Info('IB', 0, 'Flag', '', '', ''),
'IA': Info('IA', -1, 'Integer', '', '', '')}
infer_header_fields = infer_headers._InferHeaderFields()
inferred_infos = infer_header_fields._infer_info_fields(
variant, vcf_header_io.VcfHeader(infos=infos))
expected_infos = {'IF': Info('IF', 1, 'Float', '', '', ''),
'IA': Info('IA', None, 'Float', '', '', '')}
self.assertEqual(expected_infos, inferred_infos)
def test_infer_mismatched_format_field(self):
variant = self._get_sample_variant_format_fi_float_value()
formats = OrderedDict([
('FS', Format('FS', 1, 'String', 'desc')),
('FI', Format('FI', 2, 'Integer', 'desc')),
('FU', Format('FU', field_counts['.'], 'Float', 'desc')),
('GT', Format('GT', 2, 'Integer', 'Special GT key')),
('PS', Format('PS', 1, 'Integer', 'Special PS key'))])
infer_header_fields = infer_headers._InferHeaderFields()
corrected_format = infer_header_fields._infer_mismatched_format_field(
'FI', variant.calls[0].info.get('FI'),
vcf_header_io.VcfHeader(formats=formats).formats.get('FI'))
expected_formats = Format('FI', 2, 'Float', 'desc')
self.assertEqual(expected_formats, corrected_format)
def test_infer_mismatched_info_field_no_mismatches(self):
variant = self._get_sample_variant_info_ia_float_2_0_in_list()
infos = {'IS': Info('IS', 1, 'String', '', '', ''),
'ISI': Info('ISI', 1, 'Integer', '', '', ''),
'ISF': Info('ISF', 1, 'Float', '', '', ''),
'IF': Info('IF', 1, 'Float', '', '', ''),
'IB': Info('IB', 0, 'Flag', '', '', ''),
'IA': Info('IA', 'A', 'Integer', '', '', '')}
infer_header_fields = infer_headers._InferHeaderFields()
corrected_info = infer_header_fields._infer_mismatched_info_field(
'IA', variant.info.get('IA'),
vcf_header_io.VcfHeader(infos=infos).infos.get('IA'),
len(variant.alternate_bases))
self.assertEqual(None, corrected_info)
def test_infer_mismatched_info_field_correct_num(self):
variant = self._get_sample_variant_info_ia_cardinality_mismatch()
infos = {'IS': Info('IS', 1, 'String', '', '', ''),
'ISI': Info('ISI', 1, 'Integer', '', '', ''),
'ISF': Info('ISF', 1, 'Float', '', '', ''),
'IF': Info('IF', 1, 'Float', '', '', ''),
'IB': Info('IB', 0, 'Flag', '', '', ''),
'IA': Info('IA', -1, 'Float', '', '', '')}
infer_header_fields = infer_headers._InferHeaderFields()
corrected_info = infer_header_fields._infer_mismatched_info_field(
'IA', variant.info.get('IA'),
vcf_header_io.VcfHeader(infos=infos).infos.get('IA'),
len(variant.alternate_bases))
expected = Info('IA', None, 'Float', '', '', '')
self.assertEqual(expected, corrected_info)
def test_infer_annotation_types_no_conflicts(self):
anno_fields = ['CSQ']
header = self._get_sample_header_fields(with_annotation=True)
variant = self._get_sample_variant_1()
variant.info['CSQ'] = ['A|GENE1|100|1.2', 'TT|GENE1|101|1.3']
infer_header_fields = infer_headers._InferHeaderFields(
infer_headers=False, annotation_fields_to_infer=anno_fields)
inferred_headers = next(infer_header_fields.process(variant, header))
expected_types = {
'CSQ_Gene_TYPE': 'String',
'CSQ_Position_TYPE': 'Integer',
'CSQ_Score_TYPE': 'Float'
}
for key, item in inferred_headers.infos.items():
self.assertEqual(item['type'], expected_types[key])
self.assertEqual(len(expected_types), len(inferred_headers.infos))
def test_infer_annotation_types_with_missing(self):
anno_fields = ['CSQ']
header = self._get_sample_header_fields(with_annotation=True)
variant = self._get_sample_variant_1()
variant.info['CSQ'] = ['A||100|', 'A||101|1.3', 'A|||1.4', 'TT|||']
infer_header_fields = infer_headers._InferHeaderFields(
False, anno_fields)
inferred_headers = next(infer_header_fields.process(variant, header))
expected_types = {
'CSQ_Gene_TYPE': '.',
'CSQ_Position_TYPE': 'Integer',
'CSQ_Score_TYPE': 'Float'
}
for key, item in inferred_headers.infos.items():
self.assertEqual(item['type'], expected_types[key])
self.assertEqual(len(expected_types), len(inferred_headers.infos))
variant.info['CSQ'] = []
inferred_headers = next(infer_header_fields.process(variant, header))
expected = vcf_header_io.VcfHeader()
self.assertEqual(expected, inferred_headers)
