Python parse_individual Examples

Example #1

def test_parse_wrong_sex():
    # GIVEN a individual with wrong sex format
    sample_info = {"sample_id": "1", "sex": "flale", "phenotype": "affected"}
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #2

def test_parse_missing_phenotype():
    # GIVEN a individual without phenotype
    sample_info = {"sample_id": "1", "sex": "male"}
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #3

def test_parse_missing_sex():
    # GIVEN a individual without sex
    sample_info = {"sample_id": "1", "phenotype": "affected"}
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #4

File: test_parse_case.py Project: ninanorgren/scout

def test_parse_missing_phenotype():
    # GIVEN a individual without phenotype
    sample_info = {
        'sample_id': '1',
        'sex': 'male',
    }
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #5

File: test_parse_case.py Project: ninanorgren/scout

def test_parse_missing_sex():
    # GIVEN a individual without sex
    sample_info = {
        'sample_id': '1',
        'phenotype': 'affected',
    }
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #6

File: test_parse_case.py Project: Clinical-Genomics/scout

def test_parse_missing_phenotype():
    # GIVEN a individual without phenotype
    sample_info = {
        'sample_id': '1',
        'sex': 'male',
    }
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #7

File: test_parse_case.py Project: Clinical-Genomics/scout

def test_parse_missing_sex():
    # GIVEN a individual without sex
    sample_info = {
        'sample_id': '1',
        'phenotype': 'affected',
    }
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #8

File: test_parse_case.py Project: ninanorgren/scout

def test_parse_wrong_sex():
    # GIVEN a individual with wrong sex format
    sample_info = {
        'sample_id': '1',
        'sex': 'flale',
        'phenotype': 'affected',
    }
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)

Example #9

File: test_parse_case.py Project: Clinical-Genomics/scout

def test_parse_wrong_sex():
    # GIVEN a individual with wrong sex format
    sample_info = {
        'sample_id': '1',
        'sex': 'flale',
        'phenotype': 'affected',
    }
    # WHEN a individual is parsed
    with pytest.raises(PedigreeError):
        # THEN a PedigreeError should be raised
        parse_individual(sample_info)