def load_single(self, sample):
variants_mongo.index_variants()
vcf_files = sampleinfo_mongo.get_vcf_files()
vcf_file = vcf_files[sample]
self.__load_sample_variants(sample, vcf_file)
self.__log_single_successfully_loaded(sample)
def load_all(self):
if self.variant_type == 'orig':
client, db = mongo.get_connection()
vcf_files = sampleinfo_mongo.get_vcf_files()
# CHECK IF THE VCFS ARE ALL VALID BEFORE STARTING
for sample in vcf_files:
vcf_file = vcf_files[sample]
if not os.path.isfile(vcf_file):
self.__log_invalid_vcf_file(vcf_file)
sys.exit(1)
pending_vcf_files = []
for sample in vcf_files:
print sample
vcf_file = vcf_files[sample]
is_loaded = variants_mongo.is_sample_loaded(sample, self.variant_type, db)
if is_loaded:
self.__log_sample_already_loaded(sample)
continue
else:
self.__log_adding_sample_to_queue(sample, vcf_file)
pending_vcf_files.append((sample, vcf_file))
client.close()
elif self.variant_type == 'hotspot':
pending_vcf_files = self.__get_unsaved_hotspot_vcf_files()
num_processors = 10
self.__parallel_process_vcf_files(pending_vcf_files, num_processors)
self.__log_successfully_loaded()