def test_mom_dad_child_sibling_roles(fixture_dirname, ped_file):
families = FamiliesLoader.load_pedigree_file(fixture_dirname(ped_file))
family = families.get("f1")
role_builder = FamilyRoleBuilder(family)
role_builder.build_roles()
members = family.full_members
assert members[0].role == Role.dad
assert members[1].role == Role.mom
assert members[2].role == Role.prb
assert members[3].role == Role.sib
def _build_families_roles(families, pedigree_format):
has_unknown_roles = any([
p.role is None # or p.role == Role.unknown
for p in families.persons.values()
])
if has_unknown_roles or pedigree_format.get("ped_no_role"):
for family in families.values():
logger.debug(f"building family roles: {family.family_id}")
role_build = FamilyRoleBuilder(family)
role_build.build_roles()
families._ped_df = None
def test_handling_of_family_with_only_prb_role(fixture_dirname):
ped_file = fixture_dirname("pedigrees/pedigree_prb_only.ped")
families = FamiliesLoader.load_pedigree_file(ped_file)
family = families.get("f1")
role_builder = FamilyRoleBuilder(family)
role_builder.build_roles()
members = family.full_members
assert members[0].role == Role.dad
assert members[1].role == Role.mom
assert members[2].role == Role.prb
assert members[3].role == Role.sib
def test_child_and_spouse(fixture_dirname):
ped_file = fixture_dirname("pedigrees/pedigree_no_role_D.ped")
families = FamiliesLoader.load_pedigree_file(ped_file)
family = families.get("f1")
role_builder = FamilyRoleBuilder(family)
role_builder.build_roles()
members = family.full_members
assert members[0].role == Role.dad
assert members[1].role == Role.mom
assert members[2].role == Role.prb
assert members[3].role == Role.sib
assert members[4].role == Role.spouse
assert members[5].role == Role.child
def test_paternal_and_maternal_grandparents(fixture_dirname):
ped_file = fixture_dirname("pedigrees/pedigree_no_role_C.ped")
families = FamiliesLoader.load_pedigree_file(ped_file)
family = families.get("f1")
role_builder = FamilyRoleBuilder(family)
role_builder.build_roles()
members = family.full_members
assert members[0].role == Role.maternal_grandfather
assert members[1].role == Role.maternal_grandmother
assert members[2].role == Role.paternal_grandfather
assert members[3].role == Role.paternal_grandmother
assert members[4].role == Role.dad
assert members[5].role == Role.mom
assert members[6].role == Role.prb
assert members[7].role == Role.sib
def test_stepmom_and_stepdad(fixture_dirname):
ped_file = fixture_dirname("pedigrees/pedigree_no_role_G.ped")
families = FamiliesLoader.load_pedigree_file(ped_file)
family = families.get("f1")
role_builder = FamilyRoleBuilder(family)
role_builder.build_roles()
members = family.full_members
assert members[0].role == Role.dad
assert members[1].role == Role.mom
assert members[2].role == Role.step_dad
assert members[3].role == Role.step_mom
assert members[4].role == Role.maternal_half_sibling
assert members[5].role == Role.paternal_half_sibling
assert members[6].role == Role.prb
assert members[7].role == Role.sib
def test_maternal_and_paternal_cousins(fixture_dirname):
ped_file = fixture_dirname("pedigrees/pedigree_no_role_F.ped")
families = FamiliesLoader.load_pedigree_file(ped_file)
family = families.get("f1")
role_builder = FamilyRoleBuilder(family)
role_builder.build_roles()
members = family.full_members
assert members[0].role == Role.maternal_grandfather
assert members[1].role == Role.maternal_grandmother
assert members[2].role == Role.paternal_grandfather
assert members[3].role == Role.paternal_grandmother
assert members[4].role == Role.dad
assert members[5].role == Role.mom
assert members[6].role == Role.maternal_aunt
assert members[7].role == Role.unknown
assert members[8].role == Role.unknown
assert members[9].role == Role.paternal_uncle
assert members[10].role == Role.prb
assert members[11].role == Role.sib
assert members[12].role == Role.maternal_cousin
assert members[13].role == Role.paternal_cousin