def test_get_case_no_ind(self, vcf_file_no_ind):
case_id = os.path.basename(vcf_file_no_ind)
case_obj = get_cases(vcf_file_no_ind)[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == False
assert case_obj.tabix_index == False
individuals = case_obj.individuals
assert len(individuals) == 0
def test_get_case_no_ind(self, vcf_file_no_ind):
case_id = os.path.basename(vcf_file_no_ind)
case_obj = get_cases(vcf_file_no_ind)[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == False
assert case_obj.tabix_index == False
individuals = case_obj.individuals
assert len(individuals) == 0
def test_get_case_from_ped_indexed_vcf(self, indexed_vcf_file, ped_lines):
case_id = '636808'
case_obj = get_cases(indexed_vcf_file, case_lines=ped_lines)[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == True
assert case_obj.tabix_index == True
individuals = case_obj.individuals
assert len(individuals) == 3
ind_ids = set(['ADM1059A1', 'ADM1059A2', 'ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_case_from_indexed_vcf(self, indexed_vcf_file):
case_id = os.path.basename(indexed_vcf_file)
case_obj = get_cases(indexed_vcf_file)[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == True
assert case_obj.tabix_index == True
individuals = case_obj.individuals
assert len(individuals) == 3
ind_ids = set(['ADM1059A1', 'ADM1059A2', 'ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_case_from_gemini(self, gemini_path):
case_id = '643594'
case_obj = get_cases(gemini_path, variant_mode='gemini')[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == False
assert case_obj.tabix_index == False
individuals = case_obj.individuals
assert len(individuals) == 3
ind_ids = set(['NA12878', 'NA12882', 'NA12877'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_case_from_ped_indexed_vcf(self, indexed_vcf_file, ped_lines):
case_id = '636808'
case_obj = get_cases(indexed_vcf_file, case_lines=ped_lines)[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == True
assert case_obj.tabix_index == True
individuals = case_obj.individuals
assert len(individuals) == 3
ind_ids = set(['ADM1059A1','ADM1059A2','ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_case_from_indexed_vcf(self, indexed_vcf_file):
case_id = os.path.basename(indexed_vcf_file)
case_obj = get_cases(indexed_vcf_file)[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == True
assert case_obj.tabix_index == True
individuals = case_obj.individuals
assert len(individuals) == 3
ind_ids = set(['ADM1059A1','ADM1059A2','ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_case_from_gemini(self, gemini_path):
case_id = '643594'
case_obj = get_cases(gemini_path, variant_mode='gemini')[0]
assert case_obj.case_id == case_id
assert case_obj.compressed == False
assert case_obj.tabix_index == False
individuals = case_obj.individuals
assert len(individuals) == 3
ind_ids = set(['NA12878', 'NA12882','NA12877'])
assert ind_ids == set([ind.ind_id for ind in individuals])