def get_variants(self, project_id, variant_filter=None):
variant_filter_t = VariantFilter(**(variant_filter if variant_filter else {}))
db_query = _make_db_query(None, variant_filter)
collection = self._get_project_collection(project_id)
for variant_dict in collection.find(db_query).sort('xpos'):
variant = Variant.fromJSON(variant_dict)
if variant_filter is None:
yield variant
if passes_variant_filter(variant, variant_filter_t)[0]:
yield variant
def get_variants_in_gene(self, project_id, gene_id, variant_filter=None):
if variant_filter is None:
modified_variant_filter = {}
else:
modified_variant_filter = copy.deepcopy(variant_filter)
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = _make_db_query(None, modified_variant_filter)
collection = self._get_project_collection(project_id)
variants = []
for variant_dict in collection.find(db_query).hint([('gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)]):
variant = Variant.fromJSON(variant_dict)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
return variants