def setUp(self):
self._variant_generator = bigquery_vcf_data_converter.VariantGenerator(
)
self._schema_descriptor = bigquery_schema_descriptor.SchemaDescriptor(
_get_table_schema())
self._conflict_resolver = (
vcf_field_conflict_resolver.FieldConflictResolver())
self._row_generator = bigquery_vcf_data_converter.BigQueryRowGenerator(
self._schema_descriptor, self._conflict_resolver)
def __init__(self, annotation_id_to_annotation_names=None):
# type: (Dict[str, List[str]]) -> None
"""Initializes a `BigQueryToVariant` object.
Args:
annotation_id_to_annotation_names: A map where the key is the annotation
id (e.g., `CSQ`) and the value is a list of annotation names (e.g.,
['Consequence', 'IMPACT', 'SYMBOL']). The annotation str (e.g.,
'A|upstream_gene_variant|MODIFIER|PSMF1|||||') is reconstructed in the
same order as the annotation names.
"""
self._variant_generator = bigquery_vcf_data_converter.VariantGenerator(
annotation_id_to_annotation_names)
def test_get_variant_info_annotation(self):
variant_generator = bigquery_vcf_data_converter.VariantGenerator(
{'CSQ': ['allele', 'Consequence', 'AF', 'IMPACT']})
row = {
unicode(ColumnKeyConstants.ALTERNATE_BASES): [{
unicode(ColumnKeyConstants.ALTERNATE_BASES_ALT):
u'G',
unicode('CSQ'): [{
u'allele': 'G',
u'Consequence': u'upstream_gene_variant',
u'AF': u'',
u'IMPACT': u'MODIFIER'
}, {
u'allele': 'G',
u'Consequence': u'upstream_gene_variant',
u'AF': u'0.1',
u'IMPACT': u''
}]
}, {
unicode(ColumnKeyConstants.ALTERNATE_BASES_ALT):
u'T',
unicode('CSQ'): [{
u'allele': 'T',
u'Consequence': u'',
u'AF': u'',
u'IMPACT': u'MODIFIER'
}, {
u'allele': 'T',
u'Consequence': u'upstream_gene_variant',
u'AF': u'0.6',
u'IMPACT': u''
}]
}, {
unicode(ColumnKeyConstants.ALTERNATE_BASES_ALT):
u'TT',
unicode('CSQ'): []
}]
}
expected_variant_info = {
'CSQ': [
'G|upstream_gene_variant||MODIFIER',
'G|upstream_gene_variant|0.1|', 'T|||MODIFIER',
'T|upstream_gene_variant|0.6|'
]
}
self.assertEqual(expected_variant_info,
variant_generator._get_variant_info(row))
def setUp(self):
self._variant_generator = bigquery_vcf_data_converter.VariantGenerator(
)