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"])