Python parse_sv_frequencies Beispiele

Beispiel #1

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'])

Beispiel #2

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'])

Beispiel #3

Datei: test_frequency.py Projekt: Clinical-Genomics/scout

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'])

Beispiel #4

Datei: test_frequency.py Projekt: Clinical-Genomics/scout

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"])

Beispiel #5

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'])

Beispiel #6

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'])

Beispiel #7

Datei: test_frequency.py Projekt: Clinical-Genomics/scout

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"])

Beispiel #8

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'])