parser.add_argument('-d', dest='database_filepath', required=True, help='Path and filename of database to writ reads to.') parser.add_argument('-f', dest='force_overwrite', action='store_true', default=False, help='Overwrite previous tables with the same name.') args = parser.parse_args() toc = time.time() if args.input == '-': args.input = sys.stdin # Connect/make database db = Reads_db(db_file=args.database_filepath, recbyname=True) if ('seqs' not in db.tables) or (args.force_overwrite == True): db.create_seqs_table(overwrite=args.force_overwrite, read_header=args.header_format) if ('samples' not in db.tables) or (args.force_overwrite == True): db.create_samples_table(overwrite=args.force_overwrite) db.load_seqs(data_files=args.input, barcode_files=args.barcodes, buffer_max=args.buffer_max, read_header=args.header_format) total_t = time.time() - toc print >> sys.stderr, 'Loaded processed reads file in {0}'.format( time.strftime('%H:%M:%S', time.gmtime(total_t))) if __name__ == '__main__': pass