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
