rename erase_output force_outputdir

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__':