Merge pull request #18 from biosustain/cleanup

Cleanup

README.md

@@ -5,7 +5,7 @@
 [![Documentation Status](https://readthedocs.org/projects/cameo/badge/?version=latest)](https://readthedocs.org/projects/cameo/?badge=latest)
 
 ### Vision
-Provide a high-level python library to aid _in silico_ strain design process in metabolic engineering projects. The library provides a modular architecture that enables the efficient construction of custom analysis workflows.
+Cameo is a high-level python library developed to aid the _in silico_ strain design process in metabolic engineering projects. The library provides a modular architecture that enables the efficient construction of custom analysis workflows.
 
 ### Dependencies
 This library depends on:

benchmarks/common.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

benchmarks/flux_analysis.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

benchmarks/model.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

benchmarks/run.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

benchmarks/suite.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

cameo/__init__.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.
@@ -16,11 +16,36 @@
 """
 CAMEO: Computer Assisted Metabolic Engineering & Optimization
 
+Cameo is a high-level python library developed to aid the in silico
+strain design process in metabolic engineering projects. The library
+provides a modular architecture that enables the efficient construction
+of custom analysis workflows.
+
+Example
+-------
+
 from cameo import load_model
 
-model = load_model('../tests/data/EcoliCore.xml')
+# load a model from SBML format (can be found under cameo/tests/data)
+model = load_model('EcoliCore.xml')
+
+# solve the model and print the objective value
 solution = model.solve()
 print 'Objective value:', solution.f
+
+# Determine a set of gene deletions that will optimize the production
+# of a desired compound
+from cameo.strain_design.heuristic import GeneKnockoutOptimization
+from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
+from cameo.flux_analysis.simulation import fba
+
+objective = biomass_product_coupled_yield("Ec_biomass_iJO1366_core_53p95M",
+                                          "EX_succ_lp_e_rp_", "EX_glc_lp_e_rp_")
+optimization = GeneKnockoutOptimization(model=model, objective_function=of,
+                              simulation_method=fba, heuristic_method=inspyred.ec.GA)
+optimization.run(max_evaluations=2000, n=1,
+       mutation_rate=0.3, view=cameo.parallel.SequentialView(),
+       product="EX_succ_lp_e_rp_", num_elites=1)
 """
 
 from ._version import get_versions

cameo/config.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

cameo/exceptions.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

cameo/flux_analysis/__init__.py

@@ -1,52 +1,18 @@
 # Copyright 2014 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
-
+#
+#     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.
-from functools import partial
-from cobra.manipulation.delete import find_gene_knockout_reactions
-from cameo.flux_analysis.simulation import fba
-from cameo.exceptions import SolveError
-from cameo.util import TimeMachine
-
-
-def gene_knockout_growth(gene_id, model, threshold=10 ** -6, simulation_method=fba,
-                         normalize=True, biomass=None, biomass_flux=None, *args, **kwargs):
-
-    if biomass_flux is None:
-        s = model.solve()
-        biomass_flux = s.f
-    if not 'reference' in kwargs:
-        kwargs['reference'] = s.x_dict
-    gene = model.genes.get_by_id(gene_id)
-    knockouts = find_gene_knockout_reactions(model, [gene])
-    tm = TimeMachine()
 
-    for reaction in knockouts:
-        tm(do=partial(setattr, reaction, 'lower_bound', 0),
-           undo=partial(setattr, reaction, 'lower_bound', reaction.lower_bound))
-        tm(do=partial(setattr, reaction, 'upper_bound', 0),
-           undo=partial(setattr, reaction, 'upper_bound', reaction.upper_bound))
+from .simulation import *
+from .analysis import *
 
-    try:
-        s = simulation_method(model, *args, **kwargs)
-        f = s.get_primal_by_id(biomass)
-        if f >= threshold:
-            if normalize:
-                f = f / biomass_flux
-        else:
-            f = 0
-    except SolveError:
-        f = float('nan')
-    finally:
-        tm.reset()
 
-    return f

cameo/flux_analysis/analysis.py

@@ -1,23 +1,24 @@
 # Copyright 2014 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
-
+#
+#     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.
 
+__all__ = ['flux_variability_analysis', 'phenotypic_phase_plane', 'fbid']
+
 import itertools
 from copy import copy
 from collections import OrderedDict
 from functools import partial
 import numpy
-from cobra.core import Reaction
 from cameo import config
 from cameo.exceptions import UndefinedSolution, Infeasible, Unbounded, SolveError
 from cameo.util import TimeMachine, partition
@@ -358,7 +359,7 @@ def _production_envelope_inner(self, point):
         return point + tuple(interval)
 
 
-def fbip(model, knockouts, view=config.default_view, method="fva"):
+def fbid(model, knockouts, view=config.default_view, method="fva"):
     """
     Flux balance impact degree by Zhao et al 2013
 
@@ -370,14 +371,14 @@ def fbip(model, knockouts, view=config.default_view, method="fva"):
     """
 
     if method == "fva":
-        _fbip_fva(model, knockouts, view)
+        _fbid_fva(model, knockouts, view)
     elif method == "em":
         raise NotImplementedError("Elementary modes approach is not implemented")
     else:
         raise ValueError("%s method is not valid to compute FBIP" % method)
 
 
-def _fbip_fva(model, knockouts, view):
+def _fbid_fva(model, knockouts, view):
     tm = TimeMachine()
     for reaction in model.reactions:
         if reaction.reversibility:
@@ -409,23 +410,6 @@ def _fbip_fva(model, knockouts, view):
     return perturbation
 
 
-def reaction_component_production(model, reaction):
-    tm = TimeMachine()
-    for metabolite in reaction.metabolites:
-        test = Reaction("EX_%s_temp" % metabolite.id)
-        test._metabolites[metabolite] = -1
-        # hack frozen set from cobrapy to be able to add a reaction
-        metabolite._reaction = set(metabolite._reaction)
-        tm(do=partial(model.add_reactions, [test]), undo=partial(model.remove_reactions, [test]))
-        tm(do=partial(setattr, model, 'objective', test.id), undo=partial(setattr, model, 'objective', model.objective))
-        try:
-            print metabolite.id, "= ", model.solve().f
-        except SolveError:
-            print metabolite, " cannot be produced (reactions: %s)" % metabolite.reactions
-        finally:
-            tm.reset()
-
-
 if __name__ == '__main__':
     import time
     from cameo import load_model

cameo/flux_analysis/simulation.py

@@ -1,16 +1,19 @@
 # Copyright 2014 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
-
+#
+#     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.
+
+__all__ = ['fba', 'pfba', 'moma', 'lmoma', 'room']
+
 import sympy
 
 from functools import partial

cameo/io.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.

cameo/parallel.py

@@ -4,7 +4,7 @@
 # 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
+#     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,

cameo/solver_based_model.py

@@ -5,7 +5,7 @@
 # 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
+#     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,

cameo/strain_design/__init__.py

@@ -1,11 +1,11 @@
 # Copyright 2014 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
-
+#
+#     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.