def _build_cache(self, genotype_data_ids):
for genotype_data_id in genotype_data_ids:
genotype_data_study = \
self.gpf_instance.get_genotype_data(genotype_data_id)
assert genotype_data_study is not None, genotype_data_id
DenovoGeneSetCollectionFactory.build_collection(
genotype_data_study)
def denovo_gene_sets(local_gpf_instance):
return [
DenovoGeneSetCollectionFactory.load_collection(
local_gpf_instance.get_genotype_data("f1_group")),
DenovoGeneSetCollectionFactory.load_collection(
local_gpf_instance.get_genotype_data("f2_group")),
DenovoGeneSetCollectionFactory.load_collection(
local_gpf_instance.get_genotype_data("f3_group")),
]
def calc_gene_sets(request, local_gpf_instance, genotype_data_names, cleanup):
for dgs in genotype_data_names:
genotype_data = local_gpf_instance.get_genotype_data(dgs)
DenovoGeneSetCollectionFactory.build_collection(genotype_data)
print("PRECALCULATION COMPLETE")
def remove_gene_sets():
for dgs in genotype_data_names:
genotype_data = local_gpf_instance.get_genotype_data(dgs)
os.remove(
DenovoGeneSetCollectionFactory.denovo_gene_set_cache_file(
genotype_data.config, "phenotype"))
if cleanup:
request.addfinalizer(remove_gene_sets)
def remove_gene_sets():
for dgs in genotype_data_names:
genotype_data = fixtures_gpf_instance.get_genotype_data(dgs)
# fmt:off
cache_file = \
DenovoGeneSetCollectionFactory.denovo_gene_set_cache_file(
genotype_data.config, "phenotype"
)
# fmt:on
if os.path.exists(cache_file):
os.remove(cache_file)
def dae_calc_gene_sets(request, fixtures_gpf_instance, cleanup):
genotype_data_names = ["f1_group", "f2_group", "f3_group"]
for dgs in genotype_data_names:
genotype_data = fixtures_gpf_instance.get_genotype_data(dgs)
assert genotype_data is not None
DenovoGeneSetCollectionFactory.build_collection(genotype_data)
def remove_gene_sets():
for dgs in genotype_data_names:
genotype_data = fixtures_gpf_instance.get_genotype_data(dgs)
# fmt:off
cache_file = \
DenovoGeneSetCollectionFactory.denovo_gene_set_cache_file(
genotype_data.config, "phenotype"
)
# fmt:on
if os.path.exists(cache_file):
os.remove(cache_file)
if cleanup:
request.addfinalizer(remove_gene_sets)
def _load_cache(self):
for genotype_data_id in self.get_genotype_data_ids():
genotype_data_study = \
self.gpf_instance.get_genotype_data(genotype_data_id)
assert genotype_data_study is not None, genotype_data_id
denovo_gene_set_collection = \
DenovoGeneSetCollectionFactory.load_collection(
genotype_data_study)
self._denovo_gene_set_configs_cache[
genotype_data_id] = denovo_gene_set_collection.config
self._denovo_gene_set_collections_cache[
genotype_data_id] = denovo_gene_set_collection
def remove_gene_sets():
for dgs in genotype_data_names:
genotype_data = local_gpf_instance.get_genotype_data(dgs)
os.remove(
DenovoGeneSetCollectionFactory.denovo_gene_set_cache_file(
genotype_data.config, "phenotype"))
def denovo_gene_set_f4(local_gpf_instance):
return DenovoGeneSetCollectionFactory.load_collection(
local_gpf_instance.get_genotype_data("f4_trio"))