def test_run_VEPannotations_Pathogenic_VEP_SpAI_08(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_VEPannotation_Pathogenic.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': '0.8', 'CLINVAR': None, 'CLINVARonly': None, 'VEP': True, 'VEPrescue': None, 'VEPremove': ['missense_mutation'], 'BEDfile': None, 'VEPtag': None, 'CLINVARtag': None, 'verbose': None, 'VEPsep': None, 'SpliceAItag': None } # Run main_whiteList(args) # Tests assert [row for row in open('tests/files/main_test.out')] == [ row for row in open( 'tests/files/input_VEPannotation_Pathogenic_VEP_SpAI_08.out') ] # Clean os.remove('tests/files/main_test.out')
def test_run_whiteList_VEP_CLINVAR(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_whiteList_VEP.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': None, 'CLINVAR': True, 'CLINVARonly': None, 'VEP': True, 'VEPrescue': None, 'VEPremove': None, 'BEDfile': None, 'VEPtag': 'VEP', 'CLINVARtag': None, 'verbose': None, 'VEPsep': '~', 'SpliceAItag': None } # Run main_whiteList(args) # Tests assert [row for row in open('tests/files/main_test.out')] == [ row for row in open('tests/files/input_whiteList_VEP_CLINVAR.out') ] # Clean os.remove('tests/files/main_test.out')
def test_run_VEPannotations_CLINVAR_risk(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_VEPannotation.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': None, 'CLINVAR': True, 'CLINVARonly': ['pathogenic', 'risk_factor'], 'VEP': None, 'VEPrescue': None, 'VEPremove': None, 'BEDfile': None, 'VEPtag': None, 'CLINVARtag': None, 'verbose': None, 'VEPsep': None, 'SpliceAItag': None } # Run main_whiteList(args) # Tests assert [row for row in open('tests/files/main_test.out')] == [ row for row in open('tests/files/input_VEPannotation_CLINVAR_risk.out') ] # Clean os.remove('tests/files/main_test.out')
def test_run_whiteList_microannot_VEP_remove_double_BED(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_whiteList_microannot_BED.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': None, 'CLINVAR': None, 'CLINVARonly': None, 'VEP': True, 'VEPrescue': ['non_coding_transcript_exon_variant'], 'VEPremove': ['mature_miRNA_variant'], 'BEDfile': 'tests/files/input_BED_whiteList.bed', 'VEPtag': 'VEP', 'CLINVARtag': None, 'verbose': None, 'VEPsep': None, 'SpliceAItag': None } # Run main_whiteList(args) # Tests assert [row for row in open('tests/files/main_test.out')] == [ row for row in open( 'tests/files/input_whiteList_microannot_VEP_remove_double_BED.out') ] # Clean os.remove('tests/files/main_test.out')
def test_args_CLINVAR_conflict(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_whiteList.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': None, 'CLINVAR': None, 'CLINVARonly': ['Pathogenic'], 'VEP': None, 'VEPrescue': None, 'VEPremove': None, 'BEDfile': None, 'VEPtag': 'VEP', 'CLINVARtag': None, 'verbose': None, 'VEPsep': None, 'SpliceAItag': None } # Run and Tests with pytest.raises(SystemExit) as e: assert main_whiteList(args) assert str( e.value ) == '\nERROR in parsing arguments: specify the flag "--CLINVAR" to filter by CLINVAR annotations to specify tags or keywords to whitelist\n' # Clean os.remove('tests/files/main_test.out')
def test_args_VEP_conflict(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_whiteList.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': None, 'CLINVAR': None, 'CLINVARonly': None, 'VEP': None, 'VEPrescue': ['splice_region_variant', 'non_coding_transcript_variant'], 'VEPremove': None, 'BEDfile': None, 'VEPtag': 'VEP', 'CLINVARtag': None, 'verbose': None, 'VEPsep': None, 'SpliceAItag': None } # Run and Tests with pytest.raises(SystemExit) as e: assert main_whiteList(args) assert str( e.value ) == '\nERROR in parsing arguments: specify the flag "--VEP" to filter by VEP annotations to apply rescue terms or remove additional terms\n' # Clean os.remove('tests/files/main_test.out')
def test_run_whiteList_VEP_rescue(): ''' ''' # Variables args = { 'inputfile': 'tests/files/input_whiteList_VEP.vcf', 'outputfile': 'tests/files/main_test.out', 'SpliceAI': None, 'CLINVAR': None, 'CLINVARonly': None, 'VEP': True, 'VEPrescue': [ 'TF_binding_site_variant', 'splice_region_variant', 'non_coding_transcript_variant' ], 'VEPremove': None, 'BEDfile': None, 'VEPtag': 'VEP', 'CLINVARtag': None, 'verbose': None, 'VEPsep': '~', 'SpliceAItag': None } # Run main_whiteList(args) # Tests assert [row for row in open('tests/files/main_test.out')] == [ row for row in open('tests/files/input_whiteList_VEP_rescue.out') ] # Clean os.remove('tests/files/main_test.out')