feat-met.BiGGID: add BiGG identifiers for metabolites and reactions

ComplementaryScripts/modelCuration/translateYeastGEMtoBiGGIdentifiers.m

@@ -0,0 +1,39 @@
+function modelOut = translateYeastGEMtoBiGGIdentifiers(model, option)
+% This Function is to translate the model to BIGG identifiers. In
+% particular, it replaces the content of model.mets with BiGG IDs. 
+% Inputs:  
+%           model: yeast model
+%           option: 1 is to translate just metabolites which are currently
+%                   in the BiGG database. 2 is to also add suggested BiGG
+%                   identifiers (not in BiGG) database.
+%
+% author: Sebastián N. Mendoza 15/03/2019
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+modelOut = model;
+switch option
+
+    case 1
+        %just translates those metabolites which are in the BiGG database
+        if isfield(modelOut, 'metBiGGID')
+            modelOut.mets(~cellfun(@isempty, modelOut.metBiGGID)) = modelOut.metBiGGID(~cellfun(@isempty, modelOut.metBiGGID));
+        end
+
+        if isfield(modelOut, 'rxnBiGGID')
+            modelOut.rxns(~cellfun(@isempty, modelOut.rxnBiGGID)) = modelOut.rxnBiGGID(~cellfun(@isempty, modelOut.rxnBiGGID));
+        end
+    case 2
+        %also assigns BiGG-like IDs to unmapped metabolites
+        [~,s] = xlsread('../ComplementaryData/modelCuration/globalMetDictionary.csv');
+        for i = 1:size(s,1)
+            dict = splitString(s{i},',');
+            modelOut.mets{strcmp(model.metSIDs,dict{1})==1} = dict{2};
+        end
+
+        [~,s] = xlsread('../ComplementaryData/modelCuration/globalRxnDictionary.csv');
+        for i = 1:size(s,1)
+            dict = splitString(s{i},',');
+            modelOut.rxns{strcmp(model.rxnRIDs,dict{1})==1} = dict{2};
+        end
+end
+end

ComplementaryScripts/modelCuration/translateYeastGEMtoTraditionalIdentifiers.m

@@ -0,0 +1,15 @@
+function modelOut = translateYeastGEMtoTraditionalIdentifiers(model)
+% This function is to translate the model to tradionally used identifiers 
+% in the consensus model (s_xxxx[compartment] for metabolites and r_xxxx 
+% for reactions)
+% Inputs:  
+%           model: yeast model
+%
+% author: Sebastián N. Mendoza 15/03/2019
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+modelOut = model;
+modelOut.mets = modelOut.metSIDs;
+modelOut.rxns = modelOut.rxnRIDs;
+
+end

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
-MATLAB	9.1.0.441655 (R2016b)
+MATLAB	9.0.0.341360 (R2016a)
 libSBML	5.17.0
-RAVEN_toolbox	2.1.0
-COBRA_toolbox	3.0.3
+RAVEN_toolbox	2.2.0
+COBRA_toolbox	unknown
 SBML_level	3
 SBML_version	1
 fbc_version	2