def _add_vcf_file_for_family(self, project_id, family_id, vcf_file_path, reference_populations=None):
fam = self._db.families.find_one({'project_id': project_id, 'family_id': family_id})
collection = self._db[fam['coll_name']]
indiv_id_list = fam['individuals']
for i, variant in enumerate(vcf_stuff.iterate_vcf_path(
vcf_file_path,
genotypes=True,
indiv_id_list=indiv_id_list,
)):
if i % 10000 == 0:
print i
self._annotator.annotate_variant(variant, reference_populations)
family_variant = variant.make_copy(restrict_to_genotypes=fam['individuals'])
if xbrowse_utils.is_variant_relevant_for_individuals(family_variant, fam['individuals']) is True:
self._save_variant_to_collection(family_variant, collection)
def _add_vcf_file_for_family_set(self, family_info_list, vcf_file_path, reference_populations=None):
print "Adding variants from %s" % vcf_file_path
collections = {f['family_id']: self._db[f['coll_name']] for f in family_info_list}
for collection in collections.values():
collection.drop_indexes()
indiv_id_list = [i for f in family_info_list for i in f['individuals']]
for i, variant in enumerate(vcf_stuff.iterate_vcf_path(
vcf_file_path,
genotypes=True,
indiv_id_list=indiv_id_list,
)):
if i % 1000 == 0:
print i
self._annotator.annotate_variant(variant, reference_populations)
for family in family_info_list:
family_variant = variant.make_copy(restrict_to_genotypes=family['individuals'])
if xbrowse_utils.is_variant_relevant_for_individuals(family_variant, family['individuals']):
self._save_variant_to_collection(family_variant, collections[family['family_id']])
