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