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')
