def test_parse_gnomad(one_vep97_annotated_variant):
variant = one_vep97_annotated_variant
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN assert that the right frequency is returned
assert frequencies["gnomad"] == float(variant.INFO["GNOMADAF"])
def test_parse_gnomad_popmax(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN a variant dict with a certain popmax allele frequency
variant.INFO["GNOMADAF_popmax"] = "0.05"
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN assert that the last frequency is returned
assert frequencies["gnomad_max"] == float(variant.INFO["GNOMADAF_popmax"])
def test_parse_sv_gnomad(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN a variant dict with a differenct frequencies
variant.INFO["gnomad_svAF"] = "0.01"
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN the frequencies should be returned in a dictionary
assert frequencies["gnomad"] == float(variant.INFO["gnomad_svAF"])
def test_parse_gnomad_0_freq(one_vep97_annotated_variant):
variant = one_vep97_annotated_variant
# GIVEN a variant with a gnomad frequency set to 0
variant.INFO["GNOMADAF"] = "0.000"
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN assert that the right frequency is returned
assert frequencies["gnomad"] == float(variant.INFO["GNOMADAF"])
def test_parse_frequencies(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN a variant dict with a differenct frequencies
variant.INFO['1000GAF'] = '0.01'
variant.INFO['EXACAF'] = '0.001'
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN the frequencies should be returned in a dictionary
assert frequencies['thousand_g'] == float(variant.INFO['1000GAF'])
assert frequencies['exac'] == float(variant.INFO['EXACAF'])
def test_parse_frequencies(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN a variant dict with a differenct frequencies
variant.INFO["1000GAF"] = "0.01"
variant.INFO["EXACAF"] = "0.001"
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN the frequencies should be returned in a dictionary
assert frequencies["thousand_g"] == float(variant.INFO["1000GAF"])
assert frequencies["exac"] == float(variant.INFO["EXACAF"])
def test_parse_frequencies(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN a variant dict with a differenct frequencies
variant.INFO['1000GAF'] = '0.01'
variant.INFO['EXACAF'] = '0.001'
# WHEN frequencies are parsed
frequencies = parse_frequencies(variant, [])
# THEN the frequencies should be returned in a dictionary
assert frequencies['thousand_g'] == float(variant.INFO['1000GAF'])
assert frequencies['exac'] == float(variant.INFO['EXACAF'])
