def test_get_individuals_from_vcf(self, vcf_file):
individuals = get_individuals(variant_source=vcf_file)
assert len(individuals) == 3
ind_ids = set(['ADM1059A1', 'ADM1059A2', 'ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_individuals_gemini_database(self, gemini_path):
individuals = get_individuals(variant_source=gemini_path,
variant_mode='gemini')
assert len(individuals) == 3
ind_ids = set(['NA12878', 'NA12882', 'NA12877'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_individuals_from_vcf_no_ind(self, vcf_file_no_ind):
individuals = get_individuals(variant_source=vcf_file_no_ind)
assert len(individuals) == 0
def test_get_individuals_case_lines(self, vcf_file, ped_lines):
individuals = get_individuals(variant_source=vcf_file,
case_lines=ped_lines)
assert len(individuals) == 3
ind_ids = set(['ADM1059A1', 'ADM1059A2', 'ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_individuals_from_vcf(self, vcf_file):
individuals = get_individuals(variant_source=vcf_file)
assert len(individuals) == 3
ind_ids = set(['ADM1059A1','ADM1059A2','ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_individuals_from_vcf_no_ind(self, vcf_file_no_ind):
individuals = get_individuals(variant_source=vcf_file_no_ind)
assert len(individuals) == 0
def test_get_individuals_gemini_database(self, gemini_path):
individuals = get_individuals(variant_source=gemini_path, variant_mode='gemini')
assert len(individuals) == 3
ind_ids = set(['NA12878', 'NA12882','NA12877'])
assert ind_ids == set([ind.ind_id for ind in individuals])
def test_get_individuals_case_lines(self, vcf_file, ped_lines):
individuals = get_individuals(variant_source=vcf_file, case_lines=ped_lines)
assert len(individuals) == 3
ind_ids = set(['ADM1059A1','ADM1059A2','ADM1059A3'])
assert ind_ids == set([ind.ind_id for ind in individuals])
