Merge pull request #38 from cdanielmachado/develop

integrate development branch

README.md

@@ -1,5 +1,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1048261.svg)](https://doi.org/10.5281/zenodo.1048261) [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![PyPI version](https://badge.fury.io/py/framed.svg)](https://badge.fury.io/py/framed) [![Documentation Status](http://readthedocs.org/projects/framed/badge/?version=latest)](http://framed.readthedocs.io/en/latest/?badge=latest)
 
+### Note: this package will soon be deprecated! Please check the new [ReFramed](https://github.com/cdanielmachado/reframed) package.
+
 ![FRAMED](logo_300px.png)
 
 ## A python FRAmework for Metabolic Engineering and Design
@@ -21,24 +23,6 @@
     * Calibration from metabolomics data
 * Bioprocess modeling:
     * Dynamic FBA (single and multi-species)
-* Microbial community modeling:
-	* SMETANA
-
-### Documentation
-
-For documentation and API please check: http://framed.readthedocs.io/
-
-### Instalation from PyPI (stable releases)
-
-```
-pip install framed
-```
-
-### Instalation from github (latest development release)
-
-```
-pip install https://github.com/cdanielmachado/framed/archive/master.zip
-```
 
 
 ### Credits and License

scripts/framed-deletions

@@ -8,7 +8,7 @@ from framed.cobra.deletion import deletion, deleted_genes_to_reactions
 from framed.io.sbml import load_cbmodel as sbml_read
 from framed import FBA, pFBA, MOMA, lMOMA, ROOM
 from itertools import chain
-from framed.solvers.solver import Status
+from framed.solvers.solution import Status
 import warnings
 import argparse
 import re

src/framed/bioreactor/base.py

@@ -9,7 +9,7 @@
 
 from copy import deepcopy
 from ..solvers import solver_instance
-from ..solvers.solver import Status
+from framed.solvers.solution import Status
 from scipy.integrate import ode
 import numpy
 import collections

src/framed/bioreactor/bioreactors.py

@@ -9,7 +9,7 @@
 __author__ = 'kaizhuang'
 
 from .base import Bioreactor
-from ..solvers.solver import Status
+from framed.solvers.solution import Status
 
 # value definition for oxygen_availability flag
 ANAEROBIC = 0

src/framed/cobra/ensemble.py

@@ -6,7 +6,7 @@
 
 from framed import solver_instance
 from framed.model.transformation import disconnected_metabolites
-from framed.solvers.solver import Status
+from framed.solvers.solution import Status
 from framed import load_cbmodel, save_cbmodel
 from framed import FBA, pFBA
 

src/framed/cobra/essentiality.py

@@ -7,7 +7,7 @@
 from __future__ import absolute_import
 
 from ..solvers import solver_instance
-from ..solvers.solver import Status
+from framed.solvers.solution import Status
 from .simulation import FBA
 from .deletion import gene_deletion, reaction_deletion
 

src/framed/cobra/phaseplane.py

@@ -11,7 +11,7 @@
 from builtins import object
 from .simulation import FBA
 from ..solvers import solver_instance
-from ..solvers.solver import Status
+from framed.solvers.solution import Status
 import numpy
 import matplotlib.pyplot as plt
 

src/framed/cobra/reconstruction.py

@@ -8,7 +8,8 @@
 from framed.io.sbml import _load_compartments, _load_metabolites, _load_reactions, _load_cobra_bounds, _load_cobra_objective
 from libsbml import SBMLReader, SBMLDocument, XMLNode
 from re import match
-from framed.solvers.solver import VarType, Status
+from framed.solvers.solver import VarType
+from framed.solvers.solution import Status
 from numpy import where, array
 
 

src/framed/cobra/simulation.py

@@ -5,7 +5,8 @@
 """
 
 from ..solvers import solver_instance
-from ..solvers.solver import Status, VarType
+from ..solvers.solver import VarType
+from framed.solvers.solution import Status
 from warnings import warn
 from collections import Iterable
 
@@ -42,7 +43,8 @@ def FBA(model, objective=None, minimize=False, constraints=None, solver=None, ge
     return solution
 
 
-def pFBA(model, objective=None, obj_frac=None, minimize=False, constraints=None, reactions=None, solver=None):
+def pFBA(model, objective=None, obj_frac=None, minimize=False, constraints=None, reactions=None, solver=None,
+         cleanup=True):
     """ Run a parsimonious Flux Balance Analysis (pFBA) simulation:
     
     Arguments:
@@ -102,13 +104,10 @@ def pFBA(model, objective=None, obj_frac=None, minimize=False, constraints=None,
             objective[r_id] = 1
 
     solution = solver.solve(objective, minimize=True, constraints=constraints)
-
-    #post process
-
     solver.remove_constraint('obj')
     solution.pre_solution = pre_solution
 
-    if solution.status == Status.OPTIMAL:
+    if cleanup:
         for r_id in reactions:
             if model.reactions[r_id].reversible:
                 pos, neg = r_id + '+', r_id + '-'

src/framed/cobra/strain_design.py

@@ -10,7 +10,7 @@
 from .deletion import deletion
 from .simulation import pFBA
 from .essentiality import essentiality
-from ..solvers.solver import Status
+from framed.solvers.solution import Status
 from ..solvers import solver_instance
 
 

src/framed/cobra/thermodynamics.py

@@ -9,7 +9,8 @@
 
 from framed.solvers.solver import OptimizationWarning
 from ..solvers import solver_instance
-from ..solvers.solver import Status, VarType
+from ..solvers.solver import VarType
+from framed.solvers.solution import Status
 import numpy as np
 import scipy as sp
 from collections import OrderedDict

src/framed/cobra/variability.py

@@ -7,7 +7,7 @@
 
 from collections import OrderedDict
 from ..solvers import solver_instance
-from ..solvers.solver import Status
+from framed.solvers.solution import Status
 from .simulation import FBA
 from .thermodynamics import looplessFBA
 from numpy import linspace

src/framed/community/model.py

@@ -2,7 +2,7 @@
 from collections import OrderedDict
 
 from framed.model.cbmodel import CBModel, CBReaction
-from framed.model.model import Compartment, Metabolite
+from framed.model.model import Compartment, Metabolite, ReactionType
 from ..model.model import AttrOrderedDict
 from warnings import warn
 from copy import deepcopy
@@ -262,7 +262,7 @@ def _name_pattern(object_name, organism_name):
             return "{} ({})".format(object_name, organism_name)
 
         def _copy_object(obj, org_id, compartment=None):
-            new_obj = obj.copy()
+            new_obj = deepcopy(obj)
             new_obj.id = _id_pattern(obj.id, org_id)
             new_obj.name = _name_pattern(obj.name, org_id)
             if compartment:
@@ -281,7 +281,6 @@ def _copy_object(obj, org_id, compartment=None):
             raise RuntimeError("Biomass reaction not found in models: {}".format("', '".join(models_missing_biomass)))
 
         merged_model = CBModel(self.id)
-        merged_model.biomass_reaction = None
 
         organisms_biomass_metabolites = {}
         community_metabolite_exchange_lookup = {}
@@ -329,7 +328,7 @@ def _copy_object(obj, org_id, compartment=None):
 
                             exch_id = _id_pattern("R_EX_" + m_id, "pool_blacklist")
                             exch_name = _name_pattern(met.name, "pool (blacklist) exchange")
-                            blk_rxn = CBReaction(exch_id, name=exch_name, reversible=False, is_exchange=False, is_sink=True)
+                            blk_rxn = CBReaction(exch_id, name=exch_name, reversible=False, reaction_type=ReactionType.SINK)
                             blk_rxn.stoichiometry[pool_id] = -1.0
                             community_metabolite_exchange_lookup[new_met.id] = exch_id
                             merged_model.add_reaction(blk_rxn)
@@ -341,18 +340,17 @@ def _copy_object(obj, org_id, compartment=None):
 
                         exch_id = _id_pattern("R_EX_" + m_id, "pool")
                         exch_name = _name_pattern(met.name, "pool exchange")
-                        new_rxn = CBReaction(exch_id, name=exch_name, reversible=True, is_exchange=True)
+                        new_rxn = CBReaction(exch_id, name=exch_name, reversible=True, reaction_type=ReactionType.EXCHANGE)
                         new_rxn.stoichiometry[pool_id] = -1.0
                         community_metabolite_exchange_lookup[new_met.id] = exch_id
                         merged_model.add_reaction(new_rxn)
 
             for r_id, rxn in model.reactions.items():
 
-                is_exchange = rxn.is_exchange
+                is_exchange = rxn.reaction_type == ReactionType.EXCHANGE
 
                 if not is_exchange or not self._merge_extracellular_compartments:
                     new_rxn = _copy_object(rxn, org_id)
-                    new_rxn.is_exchange = False
 
                     for m_id, coeff in rxn.stoichiometry.items():
                         m_blacklisted = m_id in self._exchanged_metabolites_blacklist
@@ -376,14 +374,14 @@ def _copy_object(obj, org_id, compartment=None):
                                 self._organisms_exchange_reactions[org_id][new_rxn.id] = cnm
 
                                 if not self.interacting:
-                                    sink_rxn = CBReaction('Sink_{}'.format(new_id), is_exchange=False, is_sink=True, reversible=False)
+                                    sink_rxn = CBReaction('Sink_{}'.format(new_id), reaction_type=ReactionType.SINK, reversible=False)
                                     sink_rxn.stoichiometry = {new_id: -1}
                                     sink_rxn.lb = 0.0
                                     merged_model.add_reaction(sink_rxn)
                                 elif m_blacklisted:
                                     pool_blacklist_id = _id_pattern(m_id, "pool_blacklist")
                                     blacklist_export_rxn = CBReaction('R_EX_BLACKLIST_{}'.format(new_id),
-                                                                      is_exchange=False, is_sink=False,
+                                                                      reaction_type=ReactionType.OTHER,
                                                                       reversible=False)
                                     blacklist_export_rxn.stoichiometry = {new_id: -1, pool_blacklist_id: 1}
                                     blacklist_export_rxn.lb = 0.0
@@ -426,7 +424,7 @@ def _copy_object(obj, org_id, compartment=None):
                         continue
 
                     new_rxn = deepcopy(rxn)
-                    new_rxn.is_exchange = True
+                    new_rxn.reaction_type = ReactionType.EXCHANGE
                     if rxn.id == model.biomass_reaction and self._create_biomass:
                         new_rxn.reversible = False
                         new_rxn.objective = False
@@ -446,7 +444,7 @@ def _copy_object(obj, org_id, compartment=None):
 
         if self._create_biomass:
             biomass_rxn = CBReaction('R_Community_Growth', name="Community Growth",
-                                     reversible=False, is_exchange=False, is_sink=True, objective=1.0)
+                                     reversible=False, reaction_type=ReactionType.SINK, objective=1.0)
             for org_biomass in organisms_biomass_metabolites.values():
                 biomass_rxn.stoichiometry[org_biomass] = -1
 

src/framed/community/model2.py

@@ -0,0 +1,130 @@
+
+from ..model.model import AttrOrderedDict, ReactionType
+from framed.model.cbmodel import CBModel, CBReaction
+from framed.model.model import Compartment, Metabolite
+
+from builtins import object
+
+
+class Community(object):
+    def __init__(self, community_id, models, copy_models=False):
+        self.id = community_id
+        self.organisms = AttrOrderedDict()
+        self._merged_model = None
+        self.reaction_map = None
+        self.metabolite_map = None
+
+        for model in models:
+            self.organisms[model.id] = model.copy() if copy_models else model
+
+    def size(self):
+        return len(self.organisms)
+
+    @property
+    def merged_model(self):
+        if self._merged_model is None:
+            self._merged_model = self.merge_models()
+
+        return self._merged_model
+
+    def merge_models(self):
+        comm_model = CBModel(self.id)
+        old_ext_comps = []
+        ext_mets = []
+        self.reaction_map = {}
+        self.metabolite_map = {}
+
+        # default IDs
+        ext_comp_id = "ext"
+        biomass_id = "community_biomass"
+        comm_growth = "community_growth"
+
+        # create external compartment
+
+        comp = Compartment(ext_comp_id, "extracellular environment", external=True)
+        comm_model.add_compartment(comp)
+
+        # community biomass
+
+        met = Metabolite(biomass_id, "Total community biomass", ext_comp_id)
+        comm_model.add_metabolite(met, clear_tmp=False)
+
+        rxn = CBReaction(comm_growth, name="Community growth rate",
+                         reversible=False, stoichiometry={biomass_id: -1},
+                         lb=0, ub=None, objective=1)
+
+        comm_model.add_reaction(rxn, clear_tmp=False)
+
+        # add each organism
+
+        for org_id, model in self.organisms.items():
+
+            def rename(old_id):
+                return "{}_{}".format(old_id, org_id)
+
+            # add internal compartments
+
+            for c_id, comp in model.compartments.items():
+                if comp.external:
+                    old_ext_comps.append(c_id)
+                else:
+                    new_comp = Compartment(rename(c_id), comp.name)
+                    comm_model.add_compartment(new_comp)
+
+            # add metabolites
+
+            for m_id, met in model.metabolites.items():
+                if met.compartment not in old_ext_comps: # if is internal
+                    new_id = rename(m_id)
+                    new_met = Metabolite(new_id, met.name, rename(met.compartment))
+                    new_met.metadata = met.metadata.copy()
+                    comm_model.add_metabolite(new_met)
+                    self.metabolite_map[(org_id, m_id)] = new_id
+
+                elif m_id not in comm_model.metabolites: # if is external but was not added yet
+                    new_met = Metabolite(m_id, met.name, ext_comp_id)
+                    new_met.metadata = met.metadata.copy()
+                    comm_model.add_metabolite(new_met, clear_tmp=False)
+                    ext_mets.append(new_met.id)
+
+            # add internal reactions
+
+            for r_id, rxn in model.reactions.items():
+
+                if rxn.reaction_type == ReactionType.EXCHANGE:
+                    continue
+
+                new_id = rename(r_id)
+                new_stoichiometry = {
+                    m_id if m_id in ext_mets else rename(m_id): coeff
+                    for m_id, coeff in rxn.stoichiometry.items()
+                }
+
+                if r_id == model.biomass_reaction:
+                    new_stoichiometry[biomass_id] = 1
+
+                new_rxn = CBReaction(
+                    new_id,
+                    name=rxn.name,
+                    reversible=rxn.reversible,
+                    stoichiometry=new_stoichiometry,
+                    reaction_type=rxn.reaction_type,
+                    lb=rxn.lb,
+                    ub=rxn.ub,
+                )
+
+                comm_model.add_reaction(new_rxn, clear_tmp=False)
+                new_rxn.metadata = rxn.metadata.copy()
+                self.reaction_map[(org_id, r_id)] = new_id
+
+        # Add exchange reactions
+
+        for m_id in ext_mets:
+            rxn = CBReaction("R_EX_{}".format(m_id),
+                             reversible=True,
+                             stoichiometry={m_id: -1},
+                             reaction_type=ReactionType.EXCHANGE)
+            comm_model.add_reaction(rxn, clear_tmp=False)
+
+        return comm_model
+