def process_batch(variant_t_batch):
vep_input_file_path = tempfile.mkstemp()[1]
vep_output_file_path = tempfile.mkstemp()[1]
vep_input_file = open(vep_input_file_path, 'w')
vcf_stuff.write_sites_vcf(vep_input_file, variant_t_batch)
vep_input_file.close()
self._run_vep(vep_input_file_path, vep_output_file_path)
with open(vep_output_file_path) as f:
ret = list(parse_vep_annotations_from_vcf(f))
os.remove(vep_input_file_path)
os.remove(vep_output_file_path)
return ret
def process_batch(variant_t_batch):
vep_input_file_path = tempfile.mkstemp()[1]
vep_output_file_path = tempfile.mkstemp()[1]
vep_input_file = open(vep_input_file_path, 'w')
vcf_stuff.write_sites_vcf(vep_input_file, variant_t_batch)
vep_input_file.close()
self._run_vep(vep_input_file_path, vep_output_file_path)
with open(vep_output_file_path) as f:
ret = list(parse_vep_annotations_from_vcf(f))
os.remove(vep_input_file_path)
os.remove(vep_output_file_path)
return ret