Merge pull request #23 from biosustain/find_shorter_heterologous_alte…

…rnatives

Adapt PathwayPredictor to also find shorter heterologous alternatives to a native pathway

cameo/api/__init__.py

@@ -25,9 +25,6 @@
 import logging
 logger = logging.getLogger(__name__)
 
-with open(os.path.join(cameo._cameo_data_path, 'metanetx.pickle')) as f:
-    _METANETX = pickle.load(f)
-
 from cameo.api.hosts import hosts
 from cameo.api.designer import design
 from cameo.api.products import products

cameo/api/designer.py

@@ -16,7 +16,7 @@
 from functools import partial
 import progressbar
 from cameo import Metabolite, Model
-from cameo.api import _METANETX as METANETX
+from cameo.data import metanetx
 from cameo.api.hosts import hosts, Host
 from cameo.api.products import products
 from cameo.strain_design.pathway_prediction import PathwayPredictor
@@ -92,7 +92,7 @@ def predict_pathways(self, product, hosts=hosts):  #TODO: make this work with a
             pbar_models = progressbar.ProgressBar(widgets=["Processing", DisplayItemsWidget([model.id for model in host.models]), progressbar.Bar(), progressbar.ETA(), progressbar.Percentage()])
             for model in pbar_models(list(host.models)):
                 # TODO: Check if product is already part of model
-                pathway_predictor = PathwayPredictor(model, universal_model=METANETX['universal_model'], mapping=METANETX['bigg2mnx'])
+                pathway_predictor = PathwayPredictor(model)
                 predicted_pathways = pathway_predictor.run(product, max_predictions=5, timeout=15*60)  # TODO adjust these numbers to something reasonable
                 pathways[(host, model)] = predicted_pathways
         return pathways

cameo/api/products.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 import difflib
-from cameo.api import _METANETX as METANETX
+from cameo.data import metanetx
 
 
 def inchi_to_svg(inchi, file=None):
@@ -49,8 +49,7 @@ def _repr_html_(self):
 class Products(object):
 
     def __init__(self):
-        metabolite_ids = [metabolite.id for metabolite in METANETX['universal_model'].metabolites]
-        self.data_frame = METANETX['chem_prop'].loc[metabolite_ids]
+        self.data_frame = metanetx.chem_prop
 
     def search(self, query):
         matches = self._search_by_source(query)

cameo/core/solver_based_model.py

@@ -176,7 +176,7 @@ def solver(self, value):
         else:
             raise not_valid_interface
         self._solver = interface.Model()
-        self._populate_solver_from_scratch()
+        self._populate_solver_from_scratch()  #FIXME: This ignores non-reaction variables and constraints
 
     @property
     def exchanges(self):

cameo/data/__init__.py

@@ -0,0 +1,13 @@
+# 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.