def from_family(family: Family, add_missing_members=True):
family_connections = FamilyConnections.from_family(
family, add_missing_members=add_missing_members
)
if not family_connections:
return [Layout._handle_broken_family_connections(family)]
if family_connections.is_connected():
logger.debug(
f"building layout for connected family: {family.family_id}")
return [Layout._build_family_layout(family, family_connections)]
layouts = []
for component in family_connections.connected_components():
members = [
m for m in family.full_members
if m.person_id in component
]
fam = Family.from_persons(members)
fc = FamilyConnections.from_family(fam)
# assert fc.is_connected(), fam.family_id
layouts.append(Layout._build_family_layout(fam, fc))
x_offset = 0.0
for layout in layouts:
layout.translate(x_offset, 0.0)
bbox = layout.get_bbox()
x_offset = bbox.max_x + IndividualWithCoordinates.SIZE + 4.0
return layouts
def produce_genotype(
chrom: str,
pos: int,
genome: Genome,
family: Family,
members_with_variant: List[str],
) -> np.array:
# TODO Add support for multiallelic variants
# This method currently assumes biallelic variants
genotype = np.zeros(shape=(2, len(family)), dtype=GENOTYPE_TYPE)
for person_id, person in family.persons.items():
index = family.members_index([person_id])
has_variant = int(person_id in members_with_variant)
ploidy = get_locus_ploidy(chrom, pos, person.sex, genome)
if ploidy == 2:
genotype[1, index] = has_variant
else:
genotype[0, index] = has_variant
genotype[1, index] = -2 # signifies haploid genotype
return genotype
def _build_families(self):
families = dict()
families_details = self.rest_client.get_all_family_details(
self._remote_study_id)
for family in families_details:
family_id = family["family_id"]
person_jsons = family["members"]
family_members = []
for person_json in person_jsons:
family_members.append(Person(**person_json))
families[family_id] = Family.from_persons(family_members)
self._families = FamiliesData.from_families(families)
def test_families_data_families_by_type(quad_persons,
multigenerational_persons,
simplex_persons, multiplex_persons):
families_data = FamiliesData.from_families({
"trio_family":
Family.from_persons(trio_persons()),
"quad_family":
Family.from_persons(quad_persons),
"multigenerational_family":
Family.from_persons(multigenerational_persons),
"simplex_family":
Family.from_persons(simplex_persons),
"multiplex_family":
Family.from_persons(multiplex_persons),
})
assert families_data.families_by_type == {
FamilyType.QUAD: {"quad_family"},
FamilyType.TRIO: {"trio_family"},
FamilyType.MULTIGENERATIONAL: {"multigenerational_family"},
FamilyType.SIMPLEX: {"simplex_family"},
FamilyType.MULTIPLEX: {"multiplex_family"},
}
def test_family_type_multigenerational(role):
persons = list(trio_persons("multigenerational"))
persons.append(
Person(
**{
"family_id": "multigenerational",
"person_id": "grandparent",
"sex": "U",
"role": str(role),
"status": 1
}))
family = Family.from_persons(persons)
assert family.family_type is FamilyType.MULTIGENERATIONAL
def family3(member7):
return Family.from_persons([member7])
def family2(member4, member5, member6):
return Family.from_persons([member4, member5, member6])
def family1(member1, member2, member3):
return Family.from_persons([member1, member2, member3])
def test_family_type_multiplex(multiplex_persons):
family = Family.from_persons(multiplex_persons)
assert family.family_type is FamilyType.MULTIPLEX
def test_family_type_simplex_2(simplex_persons_2):
family = Family.from_persons(simplex_persons_2)
assert family.family_type is FamilyType.SIMPLEX
def test_family_type_quad(quad_persons):
family = Family.from_persons(quad_persons)
assert family.family_type is FamilyType.QUAD
def test_family_type_trio():
family = Family.from_persons(trio_persons())
assert family.family_type is FamilyType.TRIO