cutN must be a positive number

PanACoTA/subcommands/annotate.py

@@ -479,7 +479,7 @@ 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=utils_argparse.positive_int, default=5,
                           help=("By default, each genome will be cut into new contigs when "
                                 "at least 5 'N' in a row are found in its sequence. "
                                 "If you don't want to "

PanACoTA/subcommands/prepare.py

@@ -312,7 +312,7 @@ def build_parser(parser):
                                 "By default, it will be saved in your "
                                 "out_dir/tmp_files.")
                           )
-    general.add_argument("--cutn", dest="cutn", type=int, default=5,
+    general.add_argument("--cutn", dest="cutn", type=utils_argparse.positive_int, default=5,
                           help=("By default, each genome will be cut into new contigs when "
                                 "at least 5 'N' in a row are found in its sequence. "
                                 "If you don't want to "

PanACoTA/utils_argparse.py

@@ -99,3 +99,15 @@ def thread_num(param):
     elif param == 0:
         return nb_cpu
     return param
+
+
+def positive_int(param):
+    try:
+        param = int(param)
+    except ValueError:
+        msg = f"error: argument --cutn: invalid int value: '{param}'"
+        raise argparse.ArgumentTypeError(msg)
+    if param < 0:
+        msg = f"error: argument --cutn must be a positive integer: invalid int value: '{param}'"
+        raise argparse.ArgumentTypeError(msg)
+    return param