Merge pull request #253 from SysBioChalmers/chore/update-toolboxes

Chore: update COBRA+RAVEN toolboxes

ComplementaryScripts/otherChanges/migrateKEGGpathways.m

@@ -0,0 +1,21 @@
+
+% Load Model:
+cd ..
+model = loadYeastModel;
+
+% Migrate KEGG pathways from 'subSystems' to 'rxnKEGGpathways'
+model.rxnKEGGPathways = cell(size(model.rxns));
+for i = 1:length(model.rxns)
+    KEGGPathways = model.subSystems{i};
+    for j = 1:length(KEGGPathways)
+        if ~isempty(KEGGPathways{j})
+            KEGGPathways{j} = KEGGPathways{j}(1:8);
+        end
+    end
+    model.rxnKEGGPathways{i} = strjoin(KEGGPathways,';');
+end
+model.subSystems = cell(size(model.rxns));
+
+% Save Model:
+saveYeastModel(model);
+cd otherChanges

ComplementaryScripts/saveYeastModel.m

@@ -60,7 +60,8 @@ function saveYeastModel(model,upDATE,allowNoGrowth)
 copyfile('tempModel.xml','../ModelFiles/xml/yeastGEM.xml')
 delete('tempModel.xml');
 writeCbModel(model,'text','../ModelFiles/txt/yeastGEM.txt');
-exportForGit(model,'yeastGEM','..',{'yml'});
+exportForGit(model,'yeastGEM','../ModelFiles',{'yml'},false,false);     % temporal
+movefile ../ModelFiles/yeastGEM.yml ../ModelFiles/yml/                  % temporal
 
 %Detect boundary metabolites and save them in a .txt file:
 fid = fopen('../ModelFiles/boundaryMets.txt','wt');

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
 MATLAB	9.7.0.1190202 (R2019b)
 libSBML	5.17.0
-RAVEN_toolbox	2.4.0
-COBRA_toolbox	commit 0303050
+RAVEN_toolbox	2.4.1
+COBRA_toolbox	commit 6c49aaf
 SBML_level	3
 SBML_version	1
 fbc_version	2