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_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_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_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']