Python parse_conservation示例

示例#1

文件： test_parse_conservation.py 项目： raonyguimaraes/scout

def test_parse_conservation(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with some GERP information
    variant.INFO['GERP++_RS_prediction_term'] = 'Conserved'
    ## WHEN parsing conservation
    ## THEN assert that the field is parsed correct
    assert parse_conservation(variant, 'GERP++_RS_prediction_term') == ['Conserved']

示例#2

def test_parse_conservation(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with some GERP information
    variant.INFO['dbNSFP_GERP___RS'] = 3.7
    ## WHEN parsing conservation
    ## THEN assert that the field is parsed correct
    assert parse_conservation(variant, 'dbNSFP_GERP___RS') == ['Conserved']

示例#3

文件： test_parse_conservation.py 项目： raonyguimaraes/scout

def test_parse_conservation_wrong_term(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with wrong GERP information
    variant.INFO['GERP++_RS_prediction_term'] = 'Conservation'
    ## WHEN parsing conservation
    ## THEN assert that nothing is returned
    assert parse_conservation(variant, 'GERP++_RS_prediction_term') == []

示例#4

文件： test_parse_conservation.py 项目： Clinical-Genomics/scout

def test_parse_conservation(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with some GERP information
    variant.INFO['dbNSFP_GERP___RS'] = 3.7
    ## WHEN parsing conservation
    ## THEN assert that the field is parsed correct
    assert parse_conservation(variant, 'dbNSFP_GERP___RS') == ['Conserved']

示例#5

文件： test_parse_conservation.py 项目： raonyguimaraes/scout

def test_parse_conservation_multiple_terms(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with multiple GERP annotations
    variant.INFO['GERP++_RS_prediction_term'] = 'Conserved, NotConserved'

    ## WHEN parsing conservation
    ## THEN assert that all terms are returned
    assert parse_conservation(variant, 'GERP++_RS_prediction_term') == ['Conserved', 'NotConserved']

示例#6

文件： test_parse_conservation.py 项目： Clinical-Genomics/scout

def test_parse_conservation_multiple_terms(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with multiple GERP annotations
    variant.INFO['dbNSFP_GERP___RS'] = 3.7, -0.34

    ## WHEN parsing conservation
    ## THEN assert that all terms are returned
    assert parse_conservation(variant, 'dbNSFP_GERP___RS') == ['Conserved', 'NotConserved']

示例#7

def test_parse_conservation_multiple_terms(cyvcf2_variant):
    variant = cyvcf2_variant
    ## GIVEN a variant with multiple GERP annotations
    variant.INFO['dbNSFP_GERP___RS'] = 3.7, -0.34

    ## WHEN parsing conservation
    ## THEN assert that all terms are returned
    assert parse_conservation(
        variant, 'dbNSFP_GERP___RS') == ['Conserved', 'NotConserved']