Merge branch 'master' into devel

Author: Midnighter

cameo/strain_design/pathway_prediction/pathway_predictor.py

@@ -294,9 +294,10 @@ def run(self, product=None, max_predictions=float("inf"), min_production=.1,
                 product_reaction = self.model.add_boundary(product, type='demand')
 
             product_reaction.lower_bound = min_production
-            counter = 1
-            while counter <= max_predictions:
-                logger.debug('Predicting pathway No. %d' % counter)
+            pathway_counter = 1
+            integer_cut_counter = 1
+            while pathway_counter <= max_predictions:
+                logger.debug('Predicting pathway No. %d' % pathway_counter)
                 try:
                     self.model.slim_optimize(error_value=None)
                 except OptimizationError as err:
@@ -314,18 +315,19 @@ def run(self, product=None, max_predictions=float("inf"), min_production=.1,
                 if len(vars_to_cut) == 0:
                     # no pathway found:
                     logger.info("It seems %s is a native product in model %s. "
-                                "Let's see if we can find better heterologous pathways." % (product, self.model))
+                                "Let's see if we can find better heterologous pathways.", product, self.model)
                     # knockout adapter with native product
                     for adapter in self.adpater_reactions:
                         if product in adapter.metabolites:
-                            logger.info('Knocking out adapter reaction %s containing native product.' % adapter)
+                            logger.info('Knocking out adapter reaction %s '
+                                        'containing native product.', adapter)
                             adapter.knock_out()
                     continue
 
                 pathway = [self.model.reactions.get_by_id(y_var.name[2:]) for y_var in vars_to_cut]
 
                 pathway_metabolites = set([m for pathway_reaction in pathway for m in pathway_reaction.metabolites])
-                logger.info('Pathway predicted: %s' % '\t'.join(
+                logger.info('Pathway predicted: %s', '\t'.join(
                     [r.build_reaction_string(use_metabolite_names=True) for r in pathway]))
                 pathway_metabolites.add(product)
 
@@ -342,10 +344,10 @@ def run(self, product=None, max_predictions=float("inf"), min_production=.1,
 
                 pathway = PathwayResult(pathway, exchanges, adapters, product_reaction)
                 if not silent:
-                    util.display_pathway(pathway, counter)
+                    util.display_pathway(pathway, pathway_counter)
 
                 integer_cut = self.model.solver.interface.Constraint(Add(*vars_to_cut),
-                                                                     name="integer_cut_" + str(counter),
+                                                                     name="integer_cut_" + str(integer_cut_counter),
                                                                      ub=len(vars_to_cut) - 1)
                 logger.debug('Adding integer cut.')
                 tm(
@@ -357,26 +359,28 @@ def run(self, product=None, max_predictions=float("inf"), min_production=.1,
                     pathway.apply(self.original_model)
                     self.original_model.objective = pathway.product.id
                     try:
-                        value = self.original_model.slim_optimize(error_value=None)
+                        production_flux = self.original_model.slim_optimize(error_value=None)
                     except OptimizationError as err:
                         logger.error(err)
                         logger.error(
-                            "Addition of pathway {} made the model unsolvable. "
-                            "Skipping pathway.".format(pathway))
+                            "Addition of pathway %r made the model unsolvable. "
+                            "Skipping pathway.", pathway)
                         continue
                     else:
-                        if value > non_zero_flux_threshold:
+                        if production_flux > non_zero_flux_threshold:
                             pathways.append(pathway)
-                            logger.info("Max flux: %.5G", value)
-                            counter += 1
+                            logger.info("Max flux: %.5G", production_flux)
+                            pathway_counter += 1
                             if callback is not None:
                                 callback(pathway)
                         else:
                             logger.warning(
                                 "Pathway %r could not be verified. Production "
                                 "flux %.5G is below the requirement %.5G. "
-                                "Skipping.", pathway, value,
+                                "Skipping.", pathway, production_flux,
                                 non_zero_flux_threshold)
+                    finally:
+                        integer_cut_counter += 1
 
             return PathwayPredictions(pathways)