Merge pull request #120 from SysBioChalmers/fix/rxnConfidenceScores

fix/rxnConfidenceScores

ComplementaryScripts/missingFields/addConfidenceScores.m

@@ -0,0 +1,45 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% model = addConfidenceScores(model)
+% Rough confidence scores for reaction
+% Reactions with pubmedID and with gene information: 3
+% Reactions with gene but without pubmedID: 2 
+% Reactions without gene but need for modelling: 1
+% Reactions without gene: 0
+% Exchange reactions: NaN
+%
+% Hongzhong Lu & Benjamín J. Sánchez
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function model = addConfidenceScores(model)
+
+rxnConfidenceScores = zeros(size(model.rxns));
+
+for i = 1:length(model.rxns)
+    if ~isempty(model.rules{i})
+        if ~isempty(model.rxnReferences{i})
+            rxnConfidenceScores(i) = 3;
+        else
+            rxnConfidenceScores(i) = 2;
+        end
+    else
+        rxnName = model.rxnNames{i};
+        if contains(rxnName,'exchange')
+            rxnConfidenceScores(i) = NaN;
+        elseif contains(rxnName,'SLIME rxn') || contains(rxnName,'pseudoreaction')
+            rxnConfidenceScores(i) = 1;
+        else
+            metNames = model.metNames(model.S(:,i) ~= 0);
+            for j = 1:length(metNames)
+                if contains(metNames{j},'backbone [') || contains(metNames{j},'chain [')
+                    rxnConfidenceScores(i) = 1;
+                end
+            end
+        end
+    end
+end
+
+model.rxnConfidenceScores = rxnConfidenceScores;
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
 MATLAB	9.4.0.813654 (R2018a)
 libSBML	5.17.0
 RAVEN_toolbox	2.0.0
-COBRA_toolbox	commit 08d1e02
+COBRA_toolbox	commit 7f88d93
 SBML_level	3
 SBML_version	1
 fbc_version	2