Convert all gene-protein-reaction (GPR) associations of a metabolic model defined in SBML to disjunctive normal form (DNF).

gpr_to_dnf.py

#!/usr/bin/env python

# Copyright (c) 2021 Moritz E. Beber
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"""
Convert all GPR associations in a metabolic model to DNF.

: author : Moritz E. Beber
: license : BSD-3-Clause

"""


import logging
import sys
import time
import cobra
from typing import List

from cobra.io import read_sbml_model, write_sbml_model
from sympy import parse_expr
from sympy.logic.boolalg import to_dnf
from tqdm import tqdm


logger = logging.getLogger()


def convert_gpr_to_dnf(model: cobra.Model) -> None:
    """
    Convert all existing GPR associations to DNF.

    RBApy can only work with the disjunctive normal form (DNF) of a
    gene-protein-reaction (GPR) association.

    """
    for rxn in tqdm(model.reactions):
        if not rxn.gene_reaction_rule:
            continue
        rule = rxn.gene_reaction_rule.replace("or", "|").replace("and", "&")
        expr = parse_expr(rule, evaluate=False)
        rxn.gene_reaction_rule = str(to_dnf(expr)).replace("|", "or").replace("&", "and")


def main(argv: List[str]) -> None:
    """Manage the model conversion."""
    logger.info("Loading model from SBML...")
    start = time.perf_counter()
    model = read_sbml_model(sys.argv[1])
    logger.info("%.2f s", time.perf_counter() - start)
    logger.info("Converting all GPR assocations to DNF.")
    convert_gpr_to_dnf(model)
    logger.info("Writing model to SBML...")
    start = time.perf_counter()
    write_sbml_model(model, sys.argv[2])
    logger.info("%.2f s", time.perf_counter() - start)


if __name__ == "__main__":
    logging.basicConfig(level="INFO", format="[%(levelname)s] %(message)s")
    if len(sys.argv) != 3:
        logger.critical("Usage: %s <input model> <output model>", sys.argv[0])
        sys.exit(2)
    main(sys.argv[1:])