Merge pull request #2191 from ithiele/it_21_11_2023c

changes to generateMetaboScore

Author: ithiele

src/reconstruction/metaboRePort/generateMetaboScore.m

@@ -45,7 +45,7 @@
         DmR = DmR + 1;
     elseif  ~isempty(find(contains(model.rxns{i},'Sink_'))) || ~isempty(find(contains(model.rxns{i},'sink_')))
         SinkR = SinkR + 1;
-    elseif  ~isempty(find(contains(model.rxns{i},'biomass')))
+    elseif  ~isempty(find(contains(lower(model.rxns{i}),'biomass')))
         % Biomass Reactions SBO:0000629 Presence
         BioR = BioR + 1;
     else
@@ -95,16 +95,17 @@
 modelProp.Details.SinkRxns = [model.rxns(contains(model.rxns,'Sink_'));model.rxns(contains(model.rxns,'sink_'))];
 % biomass reactions
 modelProp.BiomassRxns = BioR;
-modelProp.Details.BiomassRxns = model.rxns(contains(model.rxns,'biomass'));% exclude EX_biomass?
+modelProp.Details.BiomassRxns = model.rxns(contains(lower(model.rxns,'biomass')));% exclude EX_biomass?
 
 modelProp.MetabolicRxns = MetR;
 modelProp.Details.MetabolicRxns =MetRxns';
 modelProp.TransportRxns = TransR;
 modelProp.Details.TransportRxns =TransRxns';
 
-% reactions without GPR - TODO should be only internal reactions
+% internal reactions without GPR 
 RxnsWOGpr = model.rxns(find(cellfun(@isempty,model.grRules)));
-
+External = [modelProp.Details.ExchangeRxns;modelProp.Details.DemandRxns;modelProp.Details.SinkRxns ;modelProp.Details.BiomassRxns ];
+RxnsWOGpr = setdiff(RxnsWOGpr,External);
 modelProp.RxnsWithoutGpr = length(RxnsWOGpr)*100/modelProp.n;
 modelProp.Details.RxnsWithoutGpr = RxnsWOGpr;