def test_deletion():
"""
Test how build vep string behaves with a deletion
"""
vep_headers = ["Allele", "Feature_type", "Consequence", "SYMBOL"]
annotation = [
"-|Transcript|downstream_gene_variant|NOC2L",
"-|Transcript|inframe_deletion|SAMD11"
]
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='ACC',
alternatives=['C'],
vep_columns=vep_headers
)
assert vep_dict['C'] == [
{'Allele': '-',
'Consequence': 'downstream_gene_variant',
'Feature_type': 'Transcript',
'SYMBOL': 'NOC2L'
},
{'Allele': '-',
'Consequence': 'inframe_deletion',
'Feature_type': 'Transcript',
'SYMBOL': 'SAMD11'
}
]
def test_build_multiple_string():
"""
Test how the build_vep_string behaves with a substitution with multiple vep
annotations.
"""
vep_headers = ["Position", "Type", "Allele"]
annotation = [
"1|nonsynonymous|C",
"1|synonymous|G",
]
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='A',
alternatives=['C','G'],
vep_columns=vep_headers
)
assert vep_dict['C'] == [{
"Position":"1",
"Type":"nonsynonymous",
"Allele":"C"
}]
assert vep_dict['G'] == [{
"Position":"1",
"Type":"synonymous",
"Allele":"G"
}]
def test_insertion():
"""
Test how build vep string behaves with a insertion.
Input of alternatives are in the VCF format.
"""
vep_headers = ["Allele", "Feature_type", "Consequence", "SYMBOL"]
annotation = [
"ACC|Transcript|downstream_gene_variant|NOC2L",
]
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='C',
alternatives=['CACC'],
vep_columns=vep_headers
)
assert vep_dict['CACC'] == [
{'Allele': 'ACC',
'Consequence': 'downstream_gene_variant',
'Feature_type': 'Transcript',
'SYMBOL': 'NOC2L'
}
]
def test_multiple_deletions():
"""
Test how build vep string behaves with multiple deletions
"""
vep_headers = ["Allele", "Feature_type", "SYMBOL"]
annotation = [
"ACTT|Transcript|NOC2L",
"ACT|Transcript|NOC2L"
]
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='TACTTT',
alternatives=['TACT', 'TACTT'],
vep_columns=vep_headers
)
assert vep_dict['TACT'] == [
{'Allele': 'ACT',
'Feature_type': 'Transcript',
'SYMBOL': 'NOC2L'
}]
assert vep_dict['TACTT'] == [
{'Allele': 'ACTT',
'Feature_type': 'Transcript',
'SYMBOL': 'NOC2L'
}
]
def test_one_deletion_and_substitution():
"""
Test how build vep string behaves with a deletion and substitution on
same position
"""
vep_headers = ["Allele", "Feature_type", "SYMBOL"]
annotation = [
"ACT|Transcript|NOC2L",
"-|Transcript|NOC2L"
]
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='ACC',
alternatives=['ACT', 'C'],
vep_columns=vep_headers
)
assert vep_dict['ACT'] == [
{'Allele': 'ACT',
'Feature_type': 'Transcript',
'SYMBOL': 'NOC2L'
}]
assert vep_dict['C'] == [
{'Allele': '-',
'Feature_type': 'Transcript',
'SYMBOL': 'NOC2L'
}
]
def test_wrong_formated_vep_annotation():
"""
Test how the build_vep_dict behaves with a wrong formatted vep annotation.
"""
vep_headers = ["Position", "Type", "Allele"]
annotation = ["1|nonsynonymous"]
with pytest.raises(SyntaxError):
vep_dict = build_vep_annotation(csq_info=annotation,
reference='A',
alternatives=['C'],
vep_columns=vep_headers)
def test_wrong_formated_vep_annotation():
"""
Test how the build_vep_dict behaves with a wrong formatted vep annotation.
"""
vep_headers = ["Position", "Type", "Allele"]
annotation = ["1|nonsynonymous"]
with pytest.raises(SyntaxError):
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='A',
alternatives=['C'],
vep_columns=vep_headers
)
def test_build_vep_dict():
"""
Test how the build_vep_dict behaves with a well formated substitution with
only one vep annotation.
"""
vep_headers = ["Position", "Type", "Allele"]
annotation = ["1|nonsynonymous|C"]
vep_dict = build_vep_annotation(csq_info=annotation,
reference='A',
alternatives=['C'],
vep_columns=vep_headers)
assert vep_dict['C'] == [{
"Position": "1",
"Type": "nonsynonymous",
"Allele": "C"
}]
def test_build_vep_dict():
"""
Test how the build_vep_dict behaves with a well formated substitution with
only one vep annotation.
"""
vep_headers = ["Position", "Type", "Allele"]
annotation = ["1|nonsynonymous|C"]
vep_dict = build_vep_annotation(
csq_info=annotation,
reference='A',
alternatives=['C'],
vep_columns=vep_headers
)
assert vep_dict['C'] == [{
"Position":"1",
"Type":"nonsynonymous",
"Allele":"C"
}]
def test_equals_sign_in_vep_consequence():
"""
Test that equals signs in vep CSQs (for example "p.=" parses correctly)
Fix from https://github.com/jamescasbon/PyVCF/issues/181
"""
vep_headers = ["Allele", "Feature_type", "HGVSp", "Consequence", "SYMBOL"]
annotation = [
"G|Transcript|p.=|downstream_gene_variant|NOC2L",
]
vep_dict = build_vep_annotation(csq_info=annotation,
reference='C',
alternatives=['G'],
vep_columns=vep_headers)
assert vep_dict['G'] == [{
'Allele': 'G',
'Consequence': 'downstream_gene_variant',
'Feature_type': 'Transcript',
'HGVSp': 'p.=',
'SYMBOL': 'NOC2L'
}]
