def test_get_consequence_types(self):
self.assertEqual(
clinvar_to_evidence_strings.get_consequence_types(
self.test_crm, self.consequence_type_dict)[0],
CT.ConsequenceType('ENSG00000139988',
CT.SoTerm('missense_variant')), '')
self.assertEqual(
clinvar_to_evidence_strings.get_consequence_types(
self.test_crm, {}), [None])
def setUp(self):
self.clinvar_record = test_clinvar.get_test_record()
report = clinvar_to_evidence_strings.Report()
consequence_type = CT.ConsequenceType("ENSG00000163646",
CT.SoTerm("stop_gained"))
# skip_record(clinvarRecord, cellbase_record, allowed_clinical_significance, counters)
self.args = [
self.clinvar_record, self.clinvar_record.measures[0],
consequence_type, "germline", ["not provided"], report
]
def test__process_consequence_type_file_tsv(self):
test_consequence_type = CT.ConsequenceType(
"ENSG00000021488", CT.SoTerm("missense_variant"))
snp_2_gene_file_path = os.path.join(os.path.dirname(__file__),
'resources',
config.snp_2_gene_file)
consequence_type_dict, one_rs_multiple_genes = \
CT.process_consequence_type_file_tsv(snp_2_gene_file_path)
self.assertEqual(consequence_type_dict["rs121908485"][0],
test_consequence_type)
def test__process_gene(self):
test_consequence_type_dict = defaultdict(list)
test_rs_id = "rs121912888"
test_ensembl_gene_id = "ENSG00000139219"
test_so_name = "missense_variant"
test_consequence_type = CT.ConsequenceType(test_ensembl_gene_id, CT.SoTerm(test_so_name))
CT.process_gene(test_consequence_type_dict, test_rs_id, test_ensembl_gene_id, test_so_name)
self.assertEqual(test_consequence_type_dict["rs121912888"][0], test_consequence_type)
def test_get_consequence_types(self):
test_consequence_type = CT.ConsequenceType("ENSG00000163646",
CT.SoTerm("stop_gained"))
self.assertEqual(
clinvar_to_evidence_strings.get_consequence_types(
self.test_crm, self.consequence_type_dict)[0],
test_consequence_type)
self.assertEqual(
clinvar_to_evidence_strings.get_consequence_types(
self.test_crm, {}), [None])
def test_set_known_mutations(self):
test_consequence_type = CT.ConsequenceType(
"ENSG00000008710", CT.SoTerm("3_prime_UTR_variant"))
self.test_ses._clear_known_mutations()
self.test_ses.set_known_mutations(test_consequence_type.so_term)
self.assertEqual(self.test_ses['evidence']['known_mutations'],
[{
'functional_consequence':
'http://purl.obolibrary.org/obo/SO_0001624',
'preferred_name': '3_prime_UTR_variant'
}])
def test__process_consequence_type_file_tsv(self):
test_consequence_type = CT.ConsequenceType("ENSG00000139988", CT.SoTerm("synonymous_variant"))
consequence_type_dict, one_rs_multiple_genes = CT.process_consequence_type_file_tsv(config.snp_2_gene_file)
self.assertEqual(consequence_type_dict["14:67729241:C:T"][0], test_consequence_type)
