def load_singlecore(args): # create a new gemini loader and populate # the gemini db and files from the VCF gemini_loader = GeminiLoader(args) gemini_loader.store_resources() gemini_loader.store_version() gemini_loader.store_vcf_header() gemini_loader.populate_from_vcf() gemini_db.add_max_aaf(gemini_loader.c) if not args.skip_gene_tables and not args.test_mode: gemini_loader.update_gene_table() if not args.test_mode: gemini_loader.build_indices_and_disconnect() if not args.no_genotypes and not args.no_load_genotypes: gemini_loader.store_sample_gt_counts()
def finalize_merged_db(tmp_db, db): ts = time.time() st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S') print st, "indexing final database." main_conn = sqlite3.connect(tmp_db) main_conn.isolation_level = None main_curr = main_conn.cursor() main_curr.execute('PRAGMA synchronous = OFF') main_curr.execute('PRAGMA journal_mode=MEMORY') gemini_db.add_max_aaf(main_curr) gemini_db.create_indices(main_curr) main_conn.commit() main_curr.close() shutil.move(tmp_db, db)