def test_build_individual():
## GIVEN information about a individual
ind_info = {
"individual_id": "1",
"father": "2",
"mother": "3",
"display_name": "1-1",
"sex": "male",
"phenotype": "affected",
"bam_file": "scout/demo/reduced_mt.bam",
"capture_kits": ["Agilent"],
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that information was parsed in the correct way
assert ind_obj["individual_id"] == ind_info["individual_id"]
assert ind_obj["display_name"] == ind_info["display_name"]
assert ind_obj["capture_kits"] == ind_info["capture_kits"]
assert ind_obj["mother"] == ind_info["mother"]
assert ind_obj["sex"] == "1"
assert ind_obj["phenotype"] == 2
assert ind_obj["bam_file"].endswith(ind_info["bam_file"])
assert ind_obj["analysis_type"] == "unknown"
def test_build_individual_wrong_analysis_type():
## GIVEN information about a individual with malformed analysis type
ind_info = {'individual_id': '1', 'analysis_type': 'hello'}
## WHEN parsing the information
## THEN assert exception is raised since we can not determin analysis type
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual():
## GIVEN information about a individual
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'display_name': '1-1',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'scout/demo/reduced_mt.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that information was parsed in the correct way
assert ind_obj['individual_id'] == ind_info['individual_id']
assert ind_obj['display_name'] == ind_info['display_name']
assert ind_obj['capture_kits'] == ind_info['capture_kits']
assert ind_obj['mother'] == ind_info['mother']
assert ind_obj['sex'] == '1'
assert ind_obj['phenotype'] == 2
assert ind_obj['bam_file'].endswith(ind_info['bam_file'])
assert ind_obj['analysis_type'] == 'unknown'
def test_build_individual_no_analysis_type():
## GIVEN information about a individual without analysis type
ind_info = {"individual_id": "1"}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert analysis type was set to unknown
assert ind_obj["analysis_type"] == "unknown"
def test_build_individual():
## GIVEN information about a individual
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'display_name': '1-1',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that information was parsed in the correct way
assert ind_obj['individual_id'] == ind_info['individual_id']
assert ind_obj['display_name'] == ind_info['display_name']
assert ind_obj['capture_kits'] == ind_info['capture_kits']
assert ind_obj['mother'] == ind_info['mother']
assert ind_obj['sex'] == '1'
assert ind_obj['phenotype'] == 2
assert ind_obj['bam_file'] == ind_info['bam_file']
assert ind_obj['analysis_type'] == 'unknown'
def test_build_individuals(parsed_case):
## GIVEN a case with multiple individuals
for ind_info in parsed_case['individuals']:
## WHEN building the ind_objs
ind_obj = build_individual(ind_info)
## THEN assert they succeded
assert ind_obj['individual_id'] == ind_info['individual_id']
assert ind_obj['display_name'] == ind_info['display_name']
assert ind_obj['capture_kits'] == ind_info['capture_kits']
def test_build_individual_no_analysis_type():
## GIVEN information about a individual without analysis type
ind_info = {
'individual_id': '1',
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert analysis type was set to unknown
assert ind_obj['analysis_type'] == 'unknown'
def test_build_individual_no_analysis_type():
## GIVEN information about a individual without analysis type
ind_info = {
'individual_id': '1',
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert analysis type was set to unknown
assert ind_obj['analysis_type'] == 'unknown'
def test_build_individuals(parsed_case):
## GIVEN a case with multiple individuals
for ind_info in parsed_case['individuals']:
## WHEN building the ind_objs
ind_obj = build_individual(ind_info)
## THEN assert they succeded
assert ind_obj['individual_id'] == ind_info['individual_id']
assert ind_obj['display_name'] == ind_info['display_name']
assert ind_obj['capture_kits'] == ind_info['capture_kits']
def test_build_individual_wrong_analysis_type():
## GIVEN information about a individual with malformed analysis type
ind_info = {
'individual_id': '1',
'analysis_type': 'hello'
}
## WHEN parsing the information
## THEN assert exception is raised since we can not determin analysis type
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_no_sex():
## GIVEN information about a individual without sex
ind_info = {
"individual_id": "1",
"father": "2",
"mother": "3",
"phenotype": "affected",
"bam_file": "a.bam",
"capture_kits": ["Agilent"],
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that sex was set to other
assert ind_obj["sex"] == "0"
def test_build_individual_no_phenotype():
## GIVEN information about a individual without phenotype
ind_info = {
"individual_id": "1",
"father": "2",
"mother": "3",
"sex": "male",
"bam_file": "a.bam",
"capture_kits": ["Agilent"],
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert phenitype was set to unknown (0)
assert ind_obj["phenotype"] == 0
def test_build_individual_no_sex():
## GIVEN information about a individual without sex
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that sex was set to other
assert ind_obj['sex'] == '0'
def test_build_individual_no_phenotype():
## GIVEN information about a individual without phenotype
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'sex': 'male',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert phenitype was set to unknown (0)
assert ind_obj['phenotype'] == 0
def test_build_individual_no_phenotype():
## GIVEN information about a individual without phenotype
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'sex': 'male',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert phenitype was set to unknown (0)
assert ind_obj['phenotype'] == 0
def test_build_individual_wrong_sex():
## GIVEN information about a individual with malformed sex information
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'sex': 'random',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
## THEN assert exception is raised since we can not determin sex
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_no_display_name():
## GIVEN information about a individual without display_name
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that individual_id was used as display name
assert ind_obj['display_name'] == ind_info['individual_id']
def test_build_individual_no_individual_id():
## GIVEN information about a individual without individual_id
ind_info = {
'father': '2',
'mother': '3',
'display_name': '1-1',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
## THEN assert exception is raised since individual_id is required
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_no_individual_id():
## GIVEN information about a individual without individual_id
ind_info = {
"father": "2",
"mother": "3",
"display_name": "1-1",
"sex": "male",
"phenotype": "affected",
"bam_file": "a.bam",
"capture_kits": ["Agilent"],
}
## WHEN parsing the information
## THEN assert exception is raised since individual_id is required
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_no_display_name():
## GIVEN information about a individual without display_name
ind_info = {
"individual_id": "1",
"father": "2",
"mother": "3",
"sex": "male",
"phenotype": "affected",
"bam_file": "a.bam",
"capture_kits": ["Agilent"],
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that individual_id was used as display name
assert ind_obj["display_name"] == ind_info["individual_id"]
def test_build_individual_wrong_sex():
## GIVEN information about a individual with malformed sex information
ind_info = {
"individual_id": "1",
"father": "2",
"mother": "3",
"sex": "random",
"phenotype": "affected",
"bam_file": "a.bam",
"capture_kits": ["Agilent"],
}
## WHEN parsing the information
## THEN assert exception is raised since we can not determin sex
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_wrong_sex():
## GIVEN information about a individual with malformed sex information
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'sex': 'random',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
## THEN assert exception is raised since we can not determin sex
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_no_sex():
## GIVEN information about a individual without sex
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that sex was set to other
assert ind_obj['sex'] == '0'
def test_build_individual_no_individual_id():
## GIVEN information about a individual without individual_id
ind_info = {
'father': '2',
'mother': '3',
'display_name': '1-1',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
## THEN assert exception is raised since individual_id is required
with pytest.raises(PedigreeError):
ind_obj = build_individual(ind_info)
def test_build_individual_no_display_name():
## GIVEN information about a individual without display_name
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent']
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that individual_id was used as display name
assert ind_obj['display_name'] == ind_info['individual_id']
def test_build_individual_tmb():
## GIVEN information about a individual
ind_info = {
"individual_id": "1",
"father": "2",
"mother": "3",
"display_name": "1-1",
"sex": "male",
"phenotype": "affected",
"bam_file": "a.bam",
"capture_kits": ["Agilent"],
"tmb": "0.1",
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that information was parsed in the correct way
assert ind_obj["tmb"] == ind_info["tmb"]
def test_build_individual_tmb():
## GIVEN information about a individual
ind_info = {
'individual_id': '1',
'father': '2',
'mother': '3',
'display_name': '1-1',
'sex': 'male',
'phenotype': 'affected',
'bam_file': 'a.bam',
'capture_kits': ['Agilent'],
'tmb': '0.1',
}
## WHEN parsing the information
ind_obj = build_individual(ind_info)
## THEN assert that information was parsed in the correct way
assert ind_obj['tmb'] == ind_info['tmb']
