feat: refactor adding of new grRules

code/curateMetsRxnsGenes.m

@@ -36,7 +36,18 @@
 %   Output:
 %       newModel    curated RAVEN model structure
 
+if nargin==4
+    error('Provide both a ''rxnsInfo'' and a ''rxnsCoeffs'' file')
+end
+if nargin<4
+    rxnsInfo='none';
+    rxnsCoeffs='none';
+end
+if nargin<3
+    genesInfo='none';
+end
 newModel=model;
+
 %% Metabolites
 if ~strcmp(metsInfo,'none')
     fid = fopen(metsInfo);
@@ -302,6 +313,9 @@
 emptyMiriam     =   all(cellfun(@isempty,miriamValues),1);
 miriamName(emptyMiriam)     = [];
 miriamValues(:,emptyMiriam) = [];
+if ~isfield(newModel,[type 'Miriams']);
+    newModel.([type 'Miriams'])=cell(numel(newModel.([type 's'])),1);
+end
 if ~isempty(miriamName)
     for i=1:numel(miriamName)
         newModel = editMiriam(newModel,type,modelIndex,miriamName{i},miriamValues(:,i),'replace');

code/modelCuration/addDBNewGeneAnnotation.m

@@ -39,12 +39,5 @@
     end
 end
 
-% Add protein name for genes
-for i = 1:length(model.genes)
-    model.proteins{i} = strcat('COBRAProtein',num2str(i));
-end
-
-% Save model:
-model = rmfield(model,'grRules');
 saveYeastModel(model)
 cd modelCuration

code/modelCuration/addTransNewGPR.m

@@ -1,42 +1,28 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % addTransNewGPR
-% Add changes from the database new anootation for new genes + manual curation on those changes
-% Input: model, databasenewGPR.tsv,SGDgeneNames.tsv.
-% As for the reference of new GPR, please find detailed information in:
-% data/databases/DBnewGeneAnnotation.tsv
-% NOTE: changeGeneAssociation.m is a function from cobra
+% Add changes from the database new anootation for new genes + manual
+% curation on those changes
+% As for the reference of new GPRs, please find detailed information in:
+% data/modelCuration/transRxnNewGPR/TransRxnNewGPR.tsv
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Load model
 cd ..
 model = loadYeastModel;
 
+% Add new genes
+newModel       = curateMetsRxnsGenes(model,'none','../data/modelCuration/transRxnNewGPR/transRxnNewGPRGenes.tsv');
+
 % Change GPR relations
-fid           = fopen('../data/modelCuration/TransRxnNewGPR.tsv');
-changegpr     = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
+fid           = fopen('../data/modelCuration/transRxnNewGPR/TransRxnNewGPR.tsv');
+changegpr     = textscan(fid,'%q %q %q','Delimiter','\t','HeaderLines',1);
 newGPR.ID     = changegpr{1};
 newGPR.GPR    = changegpr{2};
 fclose(fid);
-for i = 1:length(newGPR.ID)
-    rxnIndex = find(strcmp(model.rxns, newGPR.ID(i)));
-    model    = changeGrRules(model, model.rxns{rxnIndex}, newGPR.GPR{i});
-end
 
-% Delete unused genes (if any)
-model = deleteUnusedGenes(model);
+newModel=changeGrRules(newModel,newGPR.ID,newGPR.GPR);
 
-% Add gene standard name for new genes
-fid = fopen('../data/databases/SGDgeneNames.tsv');
-yeast_gene_annotation = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
-fclose(fid);
-for i = 1: length(model.genes)
-    geneIndex = strcmp(yeast_gene_annotation{1}, model.genes{i});
-    if sum(geneIndex) == 1 && ~isempty(yeast_gene_annotation{2}{geneIndex})
-        model.geneNames{i} = yeast_gene_annotation{2}{geneIndex};
-    else
-        model.geneNames{i} = model.genes{i};
-    end
-end
-
-saveYeastModel(model)
+% Delete unused genes (if any)
+newModel = deleteUnusedGenes(newModel);
+saveYeastModel(newModel)
 cd modelCuration