From 2dc6b57c242456c4982eb204011b7a320f9b141c Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Tue, 20 Oct 2020 10:24:36 +0200
Subject: [PATCH] Move check type of argument (percentage) to utils_argparse.py
---
PanACoTA/subcommands/corepers.py | 15 ++-------------
PanACoTA/utils_argparse.py | 13 +++++++++++++
2 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/PanACoTA/subcommands/corepers.py b/PanACoTA/subcommands/corepers.py
index d9e97bde..62756a8c 100755
--- a/PanACoTA/subcommands/corepers.py
+++ b/PanACoTA/subcommands/corepers.py
@@ -200,18 +200,7 @@ def build_parser(parser):
parser to configure in order to extract command-line arguments
"""
import argparse
-
- def percentage(param):
- try:
- param = float(param)
- except Exception:
- msg = "argument -t tol: invalid float value: {}".format(param)
- raise argparse.ArgumentTypeError(msg)
- if param < 0 or param > 1:
- msg = ("The minimum %% of genomes required in a family to be persistent must "
- "be in [0, 1]. Invalid value: {}".format(param))
- raise argparse.ArgumentTypeError(msg)
- return param
+ from PanACoTA import utils_argparse
# Create command-line parser for all options and arguments to give
required = parser.add_argument_group('Required arguments')
@@ -221,7 +210,7 @@ def build_parser(parser):
help=("Specify the output directory for your core/persistent genome."),
default=".")
optional = parser.add_argument_group('Optional arguments')
- optional.add_argument("-t", "--tol", dest="tol", default=1, type=percentage,
+ optional.add_argument("-t", "--tol", dest="tol", default=1, type=utils_argparse.percentage,
help=("min %% of genomes having at least 1 member in a family to "
"consider the family as persistent (between 0 and 1, "
"default is 1 = 100%% of genomes = Core genome)."
diff --git a/PanACoTA/utils_argparse.py b/PanACoTA/utils_argparse.py
index f553a571..8f07f939 100644
--- a/PanACoTA/utils_argparse.py
+++ b/PanACoTA/utils_argparse.py
@@ -123,3 +123,16 @@ def mash_dist(param):
msg = f"error: mash distance must be between 0 and 1: invalid value: '{param}'"
raise argparse.ArgumentTypeError(msg)
return param
+
+
+def percentage(param):
+ try:
+ param = float(param)
+ except Exception:
+ msg = "argument -t tol: invalid float value: {}".format(param)
+ raise argparse.ArgumentTypeError(msg)
+ if param < 0 or param > 1:
+ msg = ("The minimum %% of genomes required in a family to be persistent must "
+ "be in [0, 1]. Invalid value: {}".format(param))
+ raise argparse.ArgumentTypeError(msg)
+ return param
--
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