fix: ravenCobraWrapper variations on cobra fields

SysBioChalmers · Feb 13, 2024 · d737363 · d737363
1 parent 8fe29c6
commit d737363
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Showing 2 changed files with 19 additions and 18 deletions.
diff --git a/io/writeYAMLmodel.m b/io/writeYAMLmodel.m
@@ -270,6 +270,11 @@ function writeField(model,fid,fieldName,type,pos,name,preserveQuotes)
                 list = ['"' list{1} '"'];
             end
             fprintf(fid,'    %s: %s\n',name,list);
+        elseif ischar(list) && strcmp(fieldName,'subSystems')
+            if preserveQuotes
+                list = ['"' list '"'];
+            end
+            fprintf(fid,'    %s: %s\n',name,list);            
         elseif length(list) > 1 || strcmp(fieldName,'subSystems')
             if preserveQuotes
                 for j=1:numel(list)

diff --git a/struct_conversion/ravenCobraWrapper.m b/struct_conversion/ravenCobraWrapper.m
@@ -209,20 +209,24 @@
     %Mandatory RAVEN fields
     newModel.mets=model.mets;
     if ~isfield(model,'comps')
-        model.comps = unique(regexprep(model.mets,'.*\[([^\]]+)\]$','$1'));
+        %Since 'comps' field is not mandatory in COBRA, it may be required
+        %to obtain the non-redundant list of comps from metabolite ids, if
+        %'comps' field is not available
+        newModel.comps = unique(regexprep(model.mets,'.*\[([^\]]+)\]$','$1'));
+        newModel.compNames = newModel.comps;
     end
-    for i=1:numel(model.comps)
-        newModel.mets=regexprep(newModel.mets,['\[', model.comps{i}, '\]$'],'');
-        newModel.mets=regexprep(newModel.mets,['\[', model.compNames{i}, '\]$'],'');
+    for i=1:numel(newModel.comps)
+        newModel.mets=regexprep(newModel.mets,['\[', newModel.comps{i}, '\]$'],'');
+        newModel.mets=regexprep(newModel.mets,['\[', newModel.compNames{i}, '\]$'],'');
     end
 
     %In some cases (e.g. any model that uses BiGG ids as main ids), there
     %may be overlapping mets due to removal of compartment info. To avoid
     %this, we change compartments from e.g. [c] into _c
     if numel(unique(newModel.mets))~=numel(model.mets)
         newModel.mets=model.mets;
-        for i=1:numel(model.comps)
-            newModel.mets=regexprep(newModel.mets,['\[' model.comps{i} '\]$'],['_' model.comps{i}]);
+        for i=1:numel(newModel.comps)
+            newModel.mets=regexprep(newModel.mets,['\[' newModel.comps{i} '\]$'],['_' newModel.comps{i}]);
         end
     end
     %Since COBRA no longer contains rev field it is assumed that rxn is
@@ -237,15 +241,7 @@
         end
     end
     newModel.b=zeros(numel(model.mets),1);
-    if ~isfield(model,'comps')
-        %Since 'comps' field is not mandatory in COBRA, it may be required
-        %to obtain the non-redundant list of comps from metabolite ids, if
-        %'comps' field is not available
-        newModel.comps=regexprep(model.mets,'^.+\[','');
-        newModel.comps=regexprep(newModel.comps,'\]$','');
-        newModel.comps=unique(newModel.comps);
-    end
-
+
     %metComps is also mandatory, but defined later to match the order of
     %fields
 
@@ -331,9 +327,9 @@
         newModel.geneShortNames=model.geneNames;
     end
     newModel.metNames=model.metNames;
-    for i=1:numel(model.comps)
-        newModel.metNames=regexprep(newModel.metNames,['\[', model.comps{i}, '\]$'],'');
-        newModel.metNames=regexprep(newModel.metNames,['\[', model.compNames{i}, '\]$'],'');
+    for i=1:numel(newModel.comps)
+        newModel.metNames=regexprep(newModel.metNames,['\[', newModel.comps{i}, '\]$'],'');
+        newModel.metNames=regexprep(newModel.metNames,['\[', newModel.compNames{i}, '\]$'],'');
     end
     newModel.metNames=deblank(newModel.metNames);
     newModel.metComps=regexprep(model.mets,'^.+\[','');