def load_collection(cls, genotype_data_study):
"""
Loads a denovo gene set collection (from the filesystem)
for a given study.
"""
config = genotype_data_study.config
assert config is not None, genotype_data_study.id
collection = DenovoGeneSetCollection(
genotype_data_study.study_id, genotype_data_study.name, config, {
collection_id: collection_config
for collection_id, collection_config in genotype_data_study.
person_set_collection_configs.items() if collection_id in
config.denovo_gene_sets.selected_person_set_collections
})
for (person_set_collection_id
) in config.denovo_gene_sets.selected_person_set_collections:
cache_dir = cls.denovo_gene_set_cache_file(
config, person_set_collection_id)
if not os.path.exists(cache_dir):
raise EnvironmentError("Denovo gene sets caches dir '{}' "
"does not exists".format(cache_dir))
with open(cache_dir, "r") as f:
contents = json.load(f)
# change all list to sets after loading from json
contents = cls._convert_cache_innermost_types(contents, list, set)
collection.cache[person_set_collection_id] = contents
return collection
def get_all_gene_sets(self, denovo_gene_set_spec, permitted_datasets=None):
denovo_gene_set_spec = self._filter_spec(denovo_gene_set_spec,
permitted_datasets)
return DenovoGeneSetCollection.get_all_gene_sets(
list(self._denovo_gene_set_collections.values()),
denovo_gene_set_spec,
)
def test_f1_autism_get_gene_sets(denovo_gene_sets):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
denovo_gene_sets,
denovo_gene_set_spec={"f1_group": {"phenotype": ["autism"]}},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Synonymous", 1)
def test_unaffected_trio_get_gene_sets(denovo_gene_set_f4):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
[denovo_gene_set_f4],
denovo_gene_set_spec={"f4_trio": {"phenotype": ["unaffected"]}},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Synonymous", 1)
def test_missense_recurrency_get_gene_sets(denovo_gene_sets):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
denovo_gene_sets,
denovo_gene_set_spec={"f2_group": {"phenotype": ["unaffected"]}},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Missense.Recurrent", 2)
assert not name_in_gene_sets(gene_sets, "Missense.Triple")
def test_synonymous_recurrency_get_gene_sets(denovo_gene_sets):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
denovo_gene_sets,
denovo_gene_set_spec={"f2_group": {"phenotype": ["autism"]}},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Synonymous", 1)
assert not name_in_gene_sets(gene_sets, "Synonymous.Triple")
def test_f1_single_get_gene_sets(denovo_gene_sets):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
denovo_gene_sets,
denovo_gene_set_spec={"f1_group": {"phenotype": ["unaffected"]}},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Missense.Single", 2)
assert name_in_gene_sets(gene_sets, "Missense.Male", 2)
def test_autism_trio_get_gene_sets(denovo_gene_set_f4):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
[denovo_gene_set_f4],
denovo_gene_set_spec={"f4_trio": {"phenotype": ["autism"]}},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Synonymous", 1)
assert name_in_gene_sets(gene_sets, "Missense", 1)
assert name_in_gene_sets(gene_sets, "Missense.Recurrent", 1)
assert name_in_gene_sets(gene_sets, "Missense.Female", 1)
def test_missense_triple_get_gene_sets_affected_and_unaffected(
denovo_gene_sets,
):
gene_sets = DenovoGeneSetCollection.get_all_gene_sets(
denovo_gene_sets,
denovo_gene_set_spec={
"f3_group": {"phenotype": ["autism", "unaffected"]}
},
)
assert gene_sets
assert name_in_gene_sets(gene_sets, "Missense.Recurrent", 2)
assert name_in_gene_sets(gene_sets, "Missense.Triple", 2)