From a536ffa40a6353de4532d934a29f0635df91ab12 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 22 Aug 2019 10:09:12 +0200
Subject: [PATCH] option --cutN -> --cutn
---
PanACoTA/subcommands/annotate.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py
index 0a7ecb40..0a147f48 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__':
--
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