Analyze the flux (im-)balance of specific metabolites.

flux_balance.py

# -*- coding: utf-7 -*-

# Copyright 2017 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Analyze the flux (im-)balance of specific metabolites."""

from __future__ import absolute_import

from pandas import Series, DataFrame

__all__ = ("metabolite_flux_balance", "imbalance")


def metabolite_flux_balance(metabolite, solution):
    """
    Return a vector of reaction fluxes scaled by the stoichiometric coefficient.

    Parameters
    ----------
    metabolite : cobra.Metabolite
        The metabolite whose fluxes are to be investigated.
    solution : cobra.Solution
        Solution with flux values.

    Returns
    -------
    pandas.Series
        A vector with fluxes of reactions that consume or produce the given
        metabolite scaled by the corresponding stoichiometric coefficients. The
        reaction identifiers are given by the index.
    """
    rxn_ids = list()
    adj_flux = list()
    for rxn in metabolite.reactions:
        coef = rxn.get_coefficient(metabolite)
        rxn_ids.append(rxn.id)
        adj_flux.append(coef * solution.fluxes[rxn.id])
    return Series(data=adj_flux, index=rxn_ids, dtype=float, name="reaction")


def imbalance(biomass, wt_solution, mutant_solution, metabolite):
    """
    Return one row of a data frame showing flux imbalance.

    Parameters
    ----------
    biomass : cobra.Reaction
        The reaction to be associated with growth.
    wt_solution : cobra.Solution
        Wildtype solution with flux values.
    mutant_solution : cobra.Solution
        Mutant solution with flux values (could be any other kind of solution).
    metabolite : cobra.Metabolite
        The metabolite whose fluxes are to be investigated.

    Returns
    -------
    pandas.DataFrame
        A single row listing wildtype growth, mutant growth, influx (production)
        of the given metabolite in wildtype and in mutant, the difference
        between those flux values, and the difference normalized by wildtype
        influx.
    """
    wt_flux = metabolite_flux_balance(metabolite, wt_solution)
    wt_influx = wt_flux[wt_flux > 0.0].sum()
    mutant_flux = metabolite_flux_balance(metabolite, mutant_solution)
    mutant_influx = mutant_flux[mutant_flux > 0.0].sum()
    columns = ["wt-growth", "mutant-growth", "wt-influx", "mutant-influx",
              "imbalance", "norm-imbalance"]
    values = (wt_solution.fluxes[biomass.id],
              mutant_solution.fluxes[biomass.id],
              wt_influx,
              mutant_influx,
              wt_influx - mutant_influx,
              (wt_influx - mutant_influx) / wt_influx)
    return DataFrame(data=[values], columns=columns)