def test_reconstruct_annotation_str_missing_annotation_names(self):
str_builder = annotation_parser.AnnotationStrBuilder(None)
annotation_maps = [{u'Consequence': u'upstream_gene_variant'}]
with self.assertRaises(ValueError):
list(str_builder.reconstruct_annotation_str(
'CSQ', annotation_maps))
str_builder = annotation_parser.AnnotationStrBuilder(
{'CSQ2': ['Consequence', 'AF']})
annotation_maps = [{u'Consequence': u'upstream_gene_variant'}]
with self.assertRaises(ValueError):
list(str_builder.reconstruct_annotation_str(
'CSQ', annotation_maps))
def __init__(self, annotation_id_to_annotation_names=None):
# type: (Dict[str, List[str]]) -> None
"""Initializes an object of `VariantGenerator`.
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.,
['allele', '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._annotation_str_builder = annotation_parser.AnnotationStrBuilder(
annotation_id_to_annotation_names)
def test_reconstruct_annotation_str(self):
str_builder = annotation_parser.AnnotationStrBuilder({
'CSQ': ['allele', 'Consequence', 'AF', 'IMPACT'],
'CSQ_2': ['allele', 'Consequence', 'IMPACT']
})
annotation_maps = [{
u'allele': u'G',
u'Consequence': u'upstream_gene_variant',
u'AF': u'',
u'IMPACT': u'MODIFIER'
}, {
u'allele': u'G',
u'Consequence': u'upstream_gene_variant',
u'AF': u'0.1',
u'IMPACT': u''
}]
expected_annotation_strs = [
'G|upstream_gene_variant||MODIFIER', 'G|upstream_gene_variant|0.1|'
]
self.assertEqual(
expected_annotation_strs,
list(str_builder.reconstruct_annotation_str(
'CSQ', annotation_maps)))