changeGeneAssoc

 changeGeneAssoc
   Changes gene association for a defined reaction

   model       a model structure to change the gene association
   rxnID       string or cell array of reaction IDs
   geneAssoc   string of additional or replacement gene association.
               Should be written with ' and ' to indicate subunits, ' or '
               to indicate isoenzymes, and brackets '()' to separate
               different instances
   replace     true if old gene association should be replaced with new
               association. False if new gene association should be
               concatenated to the old association (optional, default true)

   model       an updated model structure

 Usage: changeGeneAssoc(model,rxnID,geneAssoc,replace)

0001 function model = changeGeneAssoc(model,rxnID,geneAssoc,replace)
0002 % changeGeneAssoc
0003 %   Changes gene association for a defined reaction
0004 %
0005 %   model       a model structure to change the gene association
0006 %   rxnID       string or cell array of reaction IDs
0007 %   geneAssoc   string of additional or replacement gene association.
0008 %               Should be written with ' and ' to indicate subunits, ' or '
0009 %               to indicate isoenzymes, and brackets '()' to separate
0010 %               different instances
0011 %   replace     true if old gene association should be replaced with new
0012 %               association. False if new gene association should be
0013 %               concatenated to the old association (optional, default true)
0014 %
0015 %   model       an updated model structure
0016 %
0017 % Usage: changeGeneAssoc(model,rxnID,geneAssoc,replace)
0018 
0019 if nargin==3
0020     replace=true;
0021 end
0022 
0023 if isstr(rxnID)
0024     rxnID={rxnID};
0025 end
0026 
0027 if ~isstr(geneAssoc)
0028     EM='geneAssoc has to be string';
0029     error(sprintf(EM))
0030 end
0031 
0032 
0033 % Add genes to model
0034 geneList=transpose(cell(unique(regexp(geneAssoc,'[)(]*|( and )*|( or )*','split')))); % Extract individual, unique genes from the geneAssoc provided
0035 geneList=geneList(~cellfun(@isempty, geneList));
0036 genesToAdd.genes=setdiff(geneList,model.genes); % Only keep the genes that are not yet part of the model.genes.
0037 if ~isempty(genesToAdd.genes)
0038     model=addGenesRaven(model,genesToAdd); % Add genes
0039 end
0040 
0041 % Find reaction and gene indices
0042 idx=getIndexes(model,rxnID,'rxns');
0043 
0044 % Change gene associations
0045 if replace==true % Replace old gene associations
0046     model.grRules(idx)=cellstr(geneAssoc);
0047 else % Add gene associations, add new gene rules after 'OR'.
0048     model.grRules(idx)=cellstr('(',[model.grRules{idx},') or (',geneAssoc,')']);
0049 end
0050 
0051 %Fix grRules and reconstruct rxnGeneMat
0052 [grRules,rxnGeneMat] = standardizeGrRules(model,true);
0053 model.grRules = grRules;
0054 model.rxnGeneMat = rxnGeneMat;
0055 end