load.py

# Copyright (C) 2019- Centre of Biological Engineering,
#     University of Minho, Portugal

# 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 <http://www.gnu.org/licenses/>.
"""
Author: Vitor Pereira

Simple example/tests for loading models
"""

import os
from mewpy.simulation import get_simulator


def load_reframed():
    """
    Loads a model with REFRAMED
    """
    DIR = os.path.dirname(os.path.realpath(__file__))
    PATH = os.path.join(DIR, '../models/optram/')
    DATA_FILE = os.path.join(PATH, "yeast_7.6-optram.xml")

    from reframed.io.sbml import load_cbmodel
    model = load_cbmodel(DATA_FILE, flavor='cobra')
    model.summary()
    simul = get_simulator(model)
    simul.summary()


def load_ec_gecko():
    """ Loads a GECKO like model from AUTOPACMEN
    """
    DIR = os.path.dirname(os.path.realpath(__file__))
    PATH = os.path.join(DIR, '../models/autopacmen/')
    DATA_FILE = os.path.join(PATH, "iJO1366_2019_06_25_GECKO.xml")

    from mewpy.model.gecko import GeckoModel
    from reframed.io.sbml import load_cbmodel
    cbmodel = load_cbmodel(DATA_FILE)
    # ='R_ER_pool_TG_'
    model = GeckoModel(cbmodel, biomass_reaction_id='R_BIOMASS_Ec_iJO1366_WT_53p95M',
                       protein_reaction_id='R_PROTRS_TG_1', common_protein_pool_id='M_prot_pool')

    simul = get_simulator(model)
    for rxn in simul.reactions:
        if "R_PROT" in rxn:
            print(rxn)


def load_cobra():
    """Load a model using COBRApy
    """
    DIR = os.path.dirname(os.path.realpath(__file__))
    PATH = os.path.join(DIR, '../models/optram/')
    DATA_FILE = os.path.join(PATH, "yeast_7.6-optram.xml")

    from cobra.io import read_sbml_model
    model = read_sbml_model(DATA_FILE)
    simul = get_simulator(model)
    simul.summary()


def load_gecko():
    """Loads yeast GECKO model using REFRAMED
    """
    from mewpy.model.gecko import GeckoModel
    model = GeckoModel('single-pool')
    simul = get_simulator(model)
    simul.summary()


def load_germ_model():
    """
    Loads a GERM model
    """
    DIR = os.path.dirname(os.path.realpath(__file__))
    PATH = os.path.join(DIR, '../models/optram/')
    DATA_FILE = os.path.join(PATH, "yeast_7.6-optram.xml")

    from mewpy.io import read_sbml
    model = read_sbml(DATA_FILE, metabolic=True, regulatory=False)
    simul = get_simulator(model)
    simul.summary()


if __name__ == "__main__":
    load_cobra()
    load_gecko()
    load_reframed()
    load_ec_gecko()