Source code for cameo.core.pathway

# Copyright 2015 Novo Nordisk Foundation Center for Biosustainability, DTU.

# 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.

"""This module implements a pathway data structure that can be added to a model for example."""

from functools import partial, reduce

import six
from pandas import DataFrame

from cobra import Metabolite, Reaction


# TODO: Load pathways from SBML and JSON
# TODO: Define the product
# TODO: Visualization with ESCHER
[docs]class Pathway(object): """ Representation of a pathway (a set of reactions) Attributes ---------- reactions: list o Reaction The list of reactions in the pathway. """ def __init__(self, reactions, *args, **kwargs): super(Pathway, self).__init__(*args, **kwargs) self.reactions = reactions @property def data_frame(self): return DataFrame([[r.build_reaction_string(True), r.lower_bound, r.upper_bound] for r in self.reactions], columns=["equation", "lower_bound", "upper_bound"], index=[r.id for r in self.reactions])
[docs] @classmethod def from_file(cls, file_path, sep="\t"): """ Read a pathway from a file. The file format is: reaction_id<sep>equation<sep>lower_limit<sep>upper_limit<sep>name<sep>comments\n The equation is defined by: coefficient * substrate_name#substrate_id + ... <=> coefficient * product_name#product_id Arguments --------- file_path: str The path to the file containing the pathway sep: str The separator between elements in the file (default: "\t") Returns ------- Pathway """ reactions = [] metabolites = {} with open(file_path, "r") as pathway: for line in pathway: if line.startswith("#"): continue line = line.strip("\n") identifier, equation, lower, upper, name, comments = line.split(sep) stoichiometry = _parse_equation(equation, metabolites) reaction = _build_reaction(identifier, stoichiometry, float(upper), float(lower), name, comments) reactions.append(reaction) return cls(reactions)
[docs] def to_file(self, file_path, sep="\t"): """ Writes the pathway to a file. Arguments --------- file_path: str The path to the file where the pathway will be written sep: str The separator between elements in the file (default: "\t") See Also -------- Pathway.from_file """ with open(file_path, "w") as output_file: for reaction in self.reactions: equation = _build_equation(reaction.metabolites) output_file.write(reaction.id + sep + equation + sep + reaction.lower_bound + sep + reaction.upper_bound + sep + reaction.name + sep + reaction.notes.get("pathway_note", "") + "\n")
[docs] def plug_model(self, model): """ Plugs the pathway to a model. Metabolites are matched in the model by id. For metabolites with no ID in the model, an exchange reaction is added to the model Arguments --------- model: cobra.Model The model to plug in the pathway """ model.add_reactions(self.reactions) metabolites = set(reduce(lambda x, y: x + y, [list(r.metabolites.keys()) for r in self.reactions], [])) exchanges = [model.add_boundary(m) for m in metabolites if len(m.reactions) == 1] for exchange in exchanges: exchange.lower_bound = 0
def _build_reaction(identifier, stoichiometry, upper, lower, name, comments): reaction = Reaction(identifier) reaction.id = identifier reaction.name = name reaction.add_metabolites(stoichiometry) reaction.upper_bound = upper reaction.lower_bound = lower reaction.notes["pathway_note"] = comments return reaction def _parse_equation(equation, metabolites): stoichiometry = {} reactants, products = equation.split(" <=> ") for reactant in reactants.split(" + "): coeff, metabolite = reactant.split(" * ") name, metabolite_id = metabolite.split("#") if metabolite_id in metabolites: met = metabolites[metabolite_id] else: metabolites[metabolite_id] = met = Metabolite(id=metabolite_id, name=name) stoichiometry[met] = -float(coeff) for product in products.split(" + "): coeff, metabolite = product.split(" * ") name, metabolite_id = metabolite.split("#") if metabolite_id in metabolites: met = metabolites[metabolite_id] else: metabolites[metabolite_id] = met = Metabolite(id=metabolite_id, name=name) stoichiometry[met] = float(coeff) return stoichiometry def _build_equation(stoichiometry): products = {m: v for m, v in six.iteritems(stoichiometry) if v > 0} reactants = {m: v for m, v in six.iteritems(stoichiometry) if v < 0} products = " + ".join(["%f * %s#%s" % (v, m.name, m.id) for m, v in six.iteritems(products)]) reactants = " + ".join(["%f * %s#%s" % (-v, m.name, m.id) for m, v in six.iteritems(reactants)]) return reactants + " <=> " + products