def parse_args():
parser = argparse.ArgumentParser(
description="Score the conservation of a single alignment file, using a single scorer.",
usage="%(prog)s [-h] [-l] scorer_name align_file [-a ALIGN_PARAMS] [-p SCORER_PARAMS]")
parser.add_argument('-l', dest='list_params', default=None,
nargs=argparse.REMAINDER,
help="list parameters for all scorers (score.py -l), or for certain defined scorers (score.py -l intrepid rate4site_eb)")
parser.add_argument('scorer_name', nargs="?",
help="conservation estimation method")
parser.add_argument('align_file', nargs="?",
help="path to alignment file to score")
parser.add_argument('-a', dest='align_params', action='append', default=[],
help="parameters associcated with align_file, can specify multiple. Specify as '-a inputName=inputValue', e.g. '-a tree_file=tree.txt'")
parser.add_argument('-p', dest='scorer_params', action='append', default=[],
help="parameters to pass to the scorer, can specify multiple. Specify as '-p paramName=paramValue', e.g. '-p use_gap_penalty=1")
parser.add_argument('-d', dest='draw', action='store_true',
help="draw visual of scores")
args = parser.parse_args()
if args.list_params is not None:
list_alignment_paramdefs()
list_scorer_paramdefs(args.list_params)
sys.exit(0)
elif not args.scorer_name or not args.align_file:
parser.print_usage()
sys.stderr.write("%s: error: too few arguments\n" % sys.argv[0])
sys.exit(1)
args.align_params = parse_params(args.align_params)
args.scorer_params = parse_params(args.scorer_params)
return args
def main():
parser = argparse.ArgumentParser(
description="Run evaluators of scoring methods using the output from batch running the scorers on a dataset(s)",
usage="%(prog)s [-h] [-l] evaluator_name dataset_name <batchscore_ids...>")
parser.add_argument('-l', dest='list_batchscore_ids', type=str,
help="list all batchscore run ids for the dataset")
parser.add_argument('evaluator_name', nargs='?',
help="name of evaluator")
parser.add_argument('dataset_name', nargs='?',
help="name of dataset")
parser.add_argument('batchscore_ids', nargs='*',
help="ids of batchscore runs to evaluate")
parser.add_argument('-p', dest='evaluator_params', action='append', default=[],
help="parameters to pass to the evaluator, can specify multiple. Specify as '-p paramName=paramValue', e.g. '-p overwrite=1")
args = parser.parse_args()
if args.list_batchscore_ids:
ba_dir = get_batchscore_dir(args.list_batchscore_ids)
fnames = os.listdir(ba_dir)
print "\n".join(sorted(x for x in fnames if os.path.isdir(os.path.join(ba_dir,x))))
sys.exit(0)
if not args.evaluator_name or not args.dataset_name:
parser.print_usage()
print "%s: error: too few arguments" % sys.argv[0]
sys.exit(1)
args.evaluator_params = parse_params(args.evaluator_params)
ev_name = args.evaluator_name
ev_fn = get_evaluator(ev_name)
ev_fn(args.dataset_name, *args.batchscore_ids, **args.evaluator_params)
