From aa2d63315906062820e7a0da412b8a8d935e4601 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Fri, 23 Jun 2017 10:49:41 +0200
Subject: [PATCH] rename erase_output force_outputdir
---
build_pop.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/build_pop.py b/build_pop.py
index 415e37c..8cfb3bc 100755
--- a/build_pop.py
+++ b/build_pop.py
@@ -28,8 +28,8 @@ def parse_args():
parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False)
parser.add_argument("-c", "--coverage", help="Coverage of reads", default=15, type=int)
parser.add_argument("-o", "--output-directory", help="Output directory", default="res")
- parser.add_argument("-e", "--erase-output", help="Delete output, if directory already exists", action='store_const',
- const=True, default=False)
+ parser.add_argument("-e", "--force-outputdir", help="Delete output directory before start, if already exists",
+ action='store_const', const=True, default=False)
parser.add_argument("-f", "--force-polymorphism", help="Force polymorphism for each SV", action='store_const',
const=True, default=False)
parser.add_argument("-a", "--haploid", help="Make a haploid genome, instead of diploid one", action="store_const",
@@ -317,10 +317,10 @@ def confirm(deletions: dict, variants: dict):
return input("Continue [Y/n]? ") in ["y", "Y", ""]
-def init(output_dir, erase_output, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism,
+def init(output_dir, force_outputdir, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism,
coverage, read_len, insert_len_mean, insert_len_sd, threads, quiet=True):
if os.path.isdir(output_dir):
- if erase_output:
+ if force_outputdir:
shutil.rmtree(output_dir)
else:
eprint("Error: output directory {0} already exists.".format(output_dir))
@@ -376,7 +376,7 @@ def main():
output_dir = args.output_directory
haploid = args.haploid
nb_inds = args.nb_inds
- erase_output = args.erase_output
+ force_outputdir = args.force_outputdir
proba_del = args.proba_del
threads = args.threads
force_polymorphism = args.force_polymorphism
@@ -386,7 +386,7 @@ def main():
insert_len_sd = args.insert_len_sd
quiet = args.quiet
- init(output_dir, erase_output, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism,
+ init(output_dir, force_outputdir, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism,
coverage, read_len, insert_len_mean, insert_len_sd, threads, quiet)
if __name__ == '__main__':
--
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