def test_parse_sv_frequencies_clingen(cyvcf2_variant): variant = cyvcf2_variant # GIVEN a variant dict with a differenct frequencies variant.INFO['clinical_genomics_mipAF'] = '0.01' variant.INFO['clinical_genomics_mipOCC'] = '0.02' # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN assert that the first frequency is returned assert frequencies['clingen_mip'] == float(variant.INFO['clinical_genomics_mipAF'])
def test_parse_sv_frequencies_clingen_benign(cyvcf2_variant): variant = cyvcf2_variant # GIVEN a variant dict with a differenct frequencies variant.INFO['clingen_cgh_benignAF'] = '0.01' variant.INFO['clingen_cgh_benign'] = '3' # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN assert that the first frequency is returned assert frequencies['clingen_cgh_benign'] == float(variant.INFO['clingen_cgh_benignAF'])
def test_parse_sv_frequencies_clingen_benign(cyvcf2_variant): variant = cyvcf2_variant # GIVEN a variant dict with a differenct frequencies variant.INFO['clingen_cgh_benignAF'] = '0.01' variant.INFO['clingen_cgh_benign'] = '3' # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN the frequencies should be returned in a dictionary assert frequencies['clingen_cgh_benignAF'] == float(variant.INFO['clingen_cgh_benignAF']) assert frequencies['clingen_cgh_benign'] == int(variant.INFO['clingen_cgh_benign'])
def test_parse_sv_frequencies_ngi(cyvcf2_variant): variant = cyvcf2_variant # GIVEN a variant dict with a differenct frequencies variant.INFO["clingen_ngiAF"] = "0.1" variant.INFO["clingen_ngiOCC"] = "0.5" variant.INFO["clingen_ngi"] = "1" # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN assert that the last frequency is returned assert frequencies["clingen_ngi"] == float(variant.INFO["clingen_ngi"])
def test_parse_sv_frequencies_ngi(cyvcf2_variant): variant = cyvcf2_variant # GIVEN a variant dict with a differenct frequencies variant.INFO['clingen_ngiAF'] = '0.1' variant.INFO['clingen_ngiOCC'] = '0.5' variant.INFO['clingen_ngi'] = '1' # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN assert that the last frequency is returned assert frequencies['clingen_ngi'] == float(variant.INFO['clingen_ngi'])
def test_parse_sv_frequencies_clingen_pathogenic(cyvcf2_variant): variant = cyvcf2_variant variant.INFO['clingen_cgh_pathogenicAF'] = '0.01' variant.INFO['clingen_cgh_pathogenic'] = '3' variant.INFO['clingen_cgh_pathogenicOCC'] = '0.1' # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN assert that the first frequency is returned assert frequencies['clingen_cgh_pathogenic'] == float(variant.INFO['clingen_cgh_pathogenicAF'])
def test_parse_sv_frequencies_clingen_pathogenic(cyvcf2_variant): variant = cyvcf2_variant variant.INFO["clingen_cgh_pathogenicAF"] = "0.01" variant.INFO["clingen_cgh_pathogenic"] = "3" variant.INFO["clingen_cgh_pathogenicOCC"] = "0.1" # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN assert that the first frequency is returned assert frequencies["clingen_cgh_pathogenic"] == float( variant.INFO["clingen_cgh_pathogenicAF"])
def test_parse_sv_frequencies_clingen_benign(cyvcf2_variant): variant = cyvcf2_variant # GIVEN a variant dict with a differenct frequencies variant.INFO['clingen_cgh_benignAF'] = '0.01' variant.INFO['clingen_cgh_benign'] = '3' # WHEN frequencies are parsed frequencies = parse_sv_frequencies(variant) # THEN the frequencies should be returned in a dictionary assert frequencies['clingen_cgh_benignAF'] == float( variant.INFO['clingen_cgh_benignAF']) assert frequencies['clingen_cgh_benign'] == int( variant.INFO['clingen_cgh_benign'])