From 22fa8f934e451dd41acfbd218aa7cc112df14bdc Mon Sep 17 00:00:00 2001
From: Sylvain Soliman <Sylvain.Soliman@inria.fr>
Date: Mon, 13 Feb 2023 15:56:13 +0100
Subject: [PATCH] Allow to call with given arguments
---
casq/celldesigner2qual.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/casq/celldesigner2qual.py b/casq/celldesigner2qual.py
index 2caa24e..7f7288b 100755
--- a/casq/celldesigner2qual.py
+++ b/casq/celldesigner2qual.py
@@ -19,6 +19,7 @@ along with this program. If not, see <https://www.gnu.org/licenses/>.
import argparse
import os.path
import sys
+from typing import List
from loguru import logger # type: ignore
@@ -30,6 +31,7 @@ from .write import write_csv, write_qual
def map_to_model(map_filename: str, model_filename: str, bma=False):
"""Do the full run with defaults arguments."""
+ main()
logger.disable("casq")
with open(map_filename, "r", encoding="utf-8") as f:
info, width, height = read_celldesigner(f)
@@ -40,7 +42,7 @@ def map_to_model(map_filename: str, model_filename: str, bma=False):
bmaExport.write_bma(model_filename, info, 1, None, False, True)
-def main():
+def main(argv: List[str] = sys.argv):
"""Run conversion using the CLI given first argument."""
parser = argparse.ArgumentParser(
description=" ".join(__doc__.splitlines()[:3]) + " GPLv3"
@@ -161,7 +163,7 @@ def main():
parser.add_argument(
"outfile", nargs="?", default=sys.stdout, help="SBML-Qual/BMA json File"
)
- args = parser.parse_args()
+ args = parser.parse_args(argv)
if not args.debug:
logger.disable("casq")
--
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