diff --git a/casq/celldesigner2qual.py b/casq/celldesigner2qual.py index 2caa24e9f6c1d7d3c3668dfaad1e156923d26103..7f7288ba4c2d4cf93ca12e3cefae7a7d75b75f81 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")