def test_from_pedigree_missing_value_in_domain(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets_incomplete_domain.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
with pytest.raises(AssertionError) as excinfo:
PersonSetCollection.from_families(
config.status, quads_f1_families,
)
assert "Domain for 'status' does not have the value 'frozenset({'affected'})'!" in str(
excinfo.value
)
def test_from_pedigree_nonexistent_domain(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets_nonexistent_domain.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
with pytest.raises(AssertionError) as excinfo:
PersonSetCollection.from_families(
config.invalid, quads_f1_families,
)
assert "Domain for 'invalid' does not have the value 'frozenset({None})'!" in \
str(excinfo.value)
def build_families_report(families):
status_collection_config = {
"id":
"status",
"name":
"Affected status",
"domain": [{
"id": "affected",
"name": "affected",
"values": ["affected"],
"color": "#e35252"
}, {
"id": "unaffected",
"name": "unaffected",
"values": ["unaffected"],
"color": "#ffffff"
}],
"default": {
"id": "unspecified",
"name": "unspecified",
"color": "#aaaaaa"
},
"sources": [{
"from": "pedigree",
"column": "status"
}]
}
status_collection_config = FrozenBox(status_collection_config)
status_collection = PersonSetCollection.from_families(
status_collection_config, families)
return FamiliesReport(families, [status_collection])
def phenotype_person_sets(variants_impl):
vvars = variants_impl("variants_impala")("backends/a")
families = vvars.families
person_sets_config = FrozenBox({
"id":
"phenotype",
"sources": [{
"from": "pedigree",
"source": "status",
}],
"default": {
"id": "unknown",
"name": "Unknown",
"color": "#aaaaaa",
},
"domain": [{
"id": "autism",
"name": "Autism",
"values": ["affected"],
"color": "#ff0000"
}, {
"id": "unaffected",
"name": "Unaffected",
"values": ["unaffected"],
"color": "#0000ff",
}]
})
person_sets = PersonSetCollection.from_families(person_sets_config,
families)
assert person_sets is not None
return person_sets
def test_get_person_color(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
status_collection = PersonSetCollection.from_families(
config.status, quads_f1_families
)
assert (
PersonSetCollection.get_person_color(
quads_f1_families.persons["prb1"], status_collection
)
== "#aabbcc"
)
def test_phenotype_person_set_continuous(
fixture_dirname, fixtures_gpf_instance
):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets_phenotype.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
quads_f1_pheno = fixtures_gpf_instance.get_phenotype_data("quads_f1")
with pytest.raises(AssertionError) as excinfo:
PersonSetCollection.from_families(
config.pheno_cont, quads_f1_families, quads_f1_pheno
)
assert "Continuous measures not allowed in person sets! (instrument1.continuous)" in \
str(excinfo.value)
# TODO Add unit test for default values in person sets (normal and phenotype)
def _build_person_set_collections(self):
person_set_collections = dict()
collections_json = self.rest_client.get_all_person_set_collections(
self._remote_study_id)
for coll_json in collections_json:
psc = PersonSetCollection.from_json(coll_json, self._families)
person_set_collections[psc.id] = psc
self._person_set_collections = person_set_collections
def test_collection_merging_ordering(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets.toml")
)
config_ext = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets_extended_roles.toml")
)
filename = fixture_dirname("studies/quads_f1/data/quads_f1.ped")
print(filename)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
role_collection = PersonSetCollection.from_families(
config.role, quads_f1_families
)
role_collection_extended = PersonSetCollection.from_families(
config_ext.role, quads_f1_families
)
merged_role_collections = PersonSetCollection.merge(
[role_collection, role_collection_extended],
quads_f1_families,
"role",
"Merged Roles Collection"
)
assert list(merged_role_collections.person_sets.keys()) == [
"0_new_role_first",
"dad",
"mom",
"prb",
"sib",
"unknown",
"z_new_role_last",
]
def get_family_pedigree(family, person_set_collection):
return [(
p.family_id,
p.person_id,
p.mom_id if p.mom_id else "0",
p.dad_id if p.dad_id else "0",
p.sex.short(),
str(p.role),
PersonSetCollection.get_person_color(p, person_set_collection),
p.layout,
p.generated,
"",
"",
) for p in family.persons.values()]
def test_produce_sets(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("sample_person_sets.toml")
)
people_sets = PersonSetCollection._produce_sets(config.status)
assert people_sets == {
"affected": PersonSet(
"affected", "Affected", {"affected_val"}, "#aabbcc", dict()
),
"unaffected": PersonSet(
"unaffected", "Unaffected", {"unaffected_val"}, "#ffffff", dict()
),
"unknown": PersonSet(
"unknown", "Unknown", {"DEFAULT"}, "#aaaaaa", dict()
),
}
def test_from_pedigree(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
status_collection = PersonSetCollection.from_families(
config.status, quads_f1_families
)
result_person_ids = set(
status_collection.person_sets["affected"].persons.keys()
)
assert result_person_ids == {
'prb2', 'sib2_3', 'sib2', 'prb1', 'sib1'
}
def _build_person_set_collection(self, person_set_collection_id):
assert person_set_collection_id in \
self.config.person_set_collections.selected_person_set_collections
collections = list()
for study in self.studies:
collections.append(
study.get_person_set_collection(person_set_collection_id))
sample_collection = self.studies[0].get_person_set_collection(
person_set_collection_id)
self.person_set_collections[person_set_collection_id] = \
PersonSetCollection.merge(
collections,
self.families,
person_set_collection_id,
sample_collection.name
)
def test_multiple_column_person_set(fixture_dirname):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets_multiple_columns.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
status_sex_collection = PersonSetCollection.from_families(
config.status_sex, quads_f1_families
)
affected_male = set(
status_sex_collection.person_sets["affected_male"].persons.keys()
)
affected_female = set(
status_sex_collection.person_sets["affected_female"].persons.keys()
)
assert affected_male == {'prb1', 'prb2'}
assert affected_female == {'sib1', 'sib2', 'sib2_3'}
def test_phenotype_person_set_categorical(
fixture_dirname, fixtures_gpf_instance
):
config = get_person_set_collections_config(
fixture_dirname("quads_f1_person_sets_phenotype.toml")
)
quads_f1_families = FamiliesLoader(
fixture_dirname("studies/quads_f1/data/quads_f1.ped")
).load()
quads_f1_pheno = fixtures_gpf_instance.get_phenotype_data("quads_f1")
pheno_categorical_collection = PersonSetCollection.from_families(
config.pheno_cat, quads_f1_families, quads_f1_pheno
)
option1 = set(
pheno_categorical_collection.person_sets["option1"].persons.keys()
)
option2 = set(
pheno_categorical_collection.person_sets["option2"].persons.keys()
)
assert option1 == {"mom1"}
assert option2 == {"prb1"}
def _build_person_set_collection(self, person_set_collection_id):
collection_config = getattr(self.config.person_set_collections,
person_set_collection_id)
self.person_set_collections[person_set_collection_id] = \
PersonSetCollection.from_families(collection_config, self.families)