"""Convert CellDesigner models to SBML-qual with a rather strict semantics.
Copyright (C) 2019, Sylvain.Soliman@inria.fr
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
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
from . import bmaExport, version
from .readCD import read_celldesigner
from .simplify import simplify_model
from .write import write_csv, write_qual
[docs]
def map_to_model(map_filename: str, model_filename: str, bma=False):
"""Do the full run with defaults arguments."""
logger.disable("casq")
with open(map_filename, "r", encoding="utf-8") as f:
info, width, height = read_celldesigner(f)
simplify_model(info, [], [])
if not bma:
write_qual(model_filename, info, width, height)
else:
bmaExport.write_bma(model_filename, info, 1, None, False, True)
[docs]
def main(argv: List[str] = None):
"""Run conversion using the CLI given first argument."""
parser = argparse.ArgumentParser(
description=" ".join(__doc__.splitlines()[:3]) + " GPLv3"
)
parser.add_argument(
"-v",
"--version",
action="version",
version=f"%(prog)s v{version}",
)
parser.add_argument(
"-D", "--debug", action="store_true", help="Display a lot of debug information"
)
parser.add_argument(
"-c",
"--csv",
action="store_true",
help="Store the species information in a separate CSV (and .bnet) file",
)
parser.add_argument(
"-s",
"--sif",
action="store_true",
help="Store the influence information in a separate SIF file",
)
parser.add_argument(
"-r",
"--remove",
metavar="S",
type=int,
default="0",
help="""Delete connected components in the resulting model if their
size is smaller than S.
A negative S leads to keep only the biggest(s) connected component(s)""",
)
parser.add_argument(
"-f",
"--fixed",
type=argparse.FileType(),
help="""A CSV file containing input values or knock-ins/knock-outs,
one per line, with name in the first column and the value in the second.""",
)
parser.add_argument(
"-n",
"--names",
action="store_true",
help="Use the names as IDs in the SBML file",
)
if sys.version_info >= (3, 8, 0):
parser.add_argument(
"-u",
"--upstream",
action="extend",
nargs="*",
type=str,
default=[],
help="Only species upstream of this/these species will be kept",
)
parser.add_argument(
"-d",
"--downstream",
action="extend",
nargs="*",
type=str,
default=[],
help="Only species downstream of this/these species will be kept",
)
else:
parser.add_argument(
"-u",
"--upstream",
action="append",
type=str,
default=[],
help="Only species upstream of this/these species will be kept",
)
parser.add_argument(
"-d",
"--downstream",
action="append",
type=str,
default=[],
help="Only species downstream of this/these species will be kept",
)
parser.add_argument(
"infile",
type=argparse.FileType("r", encoding="utf-8"),
nargs="?",
default=sys.stdin,
help="CellDesigner File",
)
parser.add_argument(
"-b",
"--bma",
action="store_true",
help="Output to BMA json format",
)
parser.add_argument(
"-g",
"--granularity",
type=int,
default="1",
help="When exporting to BMA, use this granularity",
)
parser.add_argument(
"-i",
"--input",
type=int,
default=None,
help="When exporting to BMA, nodes with no input should be set to this value",
)
parser.add_argument(
"-C",
"--colourConstant",
action="store_false",
help="When exporting to BMA, colour all variables pink (defaults to colour by compartment)",
)
parser.add_argument(
"outfile", nargs="?", default=sys.stdout, help="SBML-Qual/BMA json File"
)
if argv:
args = parser.parse_args(argv)
else:
args = parser.parse_args()
if not args.debug:
logger.disable("casq")
logger.debug("parsing {fname}…", fname=args.infile.name)
info, width, height = read_celldesigner(args.infile)
simplify_model(info, args.upstream, args.downstream, args.names)
if args.infile != sys.stdin and args.outfile == sys.stdout:
args.outfile = os.path.splitext(args.infile.name)[0] + ".sbml"
if args.bma:
bmaExport.write_bma(
args.outfile, info, args.granularity, args.input, False, args.colourConstant
)
else:
write_qual(
args.outfile,
info,
width,
height,
remove=args.remove,
sif=args.sif,
fixed=args.fixed,
)
if args.csv and args.outfile != sys.stdout:
write_csv(args.outfile, info)
if __name__ == "__main__": # pragma: no cover
main()
