diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py index 0a7ecb4070976a0e698ecb3a5662dc896f73f5ed..0a147f48fd115fa4626e7d110371c9b461246c33 100755 --- a/PanACoTA/subcommands/annotate.py +++ b/PanACoTA/subcommands/annotate.py @@ -449,7 +449,7 @@ def build_parser(parser): optional.add_argument("--nbcont", dest="nbcont", type=utils_argparse.cont_num, default=999, help=("Maximum number of contigs allowed to keep a genome. " "Default is 999.")) - optional.add_argument("--cutN", dest="cutn", type=int, default=5, + optional.add_argument("--cutn", dest="cutn", type=int, default=5, help=("By default, each genome will be cut into new contigs when " "at least 5 'N' at a stretch are found in its sequence. " "If you don't want to " @@ -541,7 +541,6 @@ def check_args(parser, args): with error message if error occurs with arguments given. """ - # Message if user kept default thresholds for L90 and nbcont. Just to warn him, to be sure # it was on purpose def thresholds_message(l90, nbcont): @@ -601,7 +600,6 @@ def check_args(parser, args): "are the 20 first characters of first word of current " "header", "yellow")) print() - return args # If db_path2 is used only with infofile if args.db_path2 and not args.info: @@ -609,6 +607,7 @@ def check_args(parser, args): "sequences come from 2 different folders (db_path and tmp_path if from a " "previous run of this module). Use --info <info-file> or " "remove '-d2 <path>' ") + return args if __name__ == '__main__':