Decompartmentalize models

decompartmentalize.py

from cameo import Model, Reaction
from re import sub
def decompartmentalize(model, rules=None):
    if rules is None:
        rules = {}
    compartmentless_model = Model()
    for reaction in model.reactions:
        new_reaction = reaction.copy()
        new_reaction.clear_metabolites()
        new_metabolites = {}
        for metabolite, coeff in reaction.metabolites.items():
            new_metabolite = metabolite.copy()
            try:
                new_compartment = rules[metabolite.compartment]
            except KeyError:
                pass
            else:
                # for bigg models
                new_metabolite.id = sub('_{}$'.format(metabolite.compartment), '_' + new_compartment, metabolite.id)
                new_metabolite.compartment = new_compartment
            new_metabolites[new_metabolite] = coeff
        new_reaction.add_metabolites(new_metabolites)
        compartmentless_model.add_reaction(new_reaction)
    return compartmentless_model