0001 function gpraModel = readSimPhenyGprText(file,model)
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0016 [tmp,tmp,rxnNames,rxnDesrs,rxnEqns,Confs,subSystems,Regions,gpraStrings,proteinStrings,ECs] = ...
0017 textread(file,'%s %s %s %s %s %s %s %s %s %s %s','delimiter','\t','headerlines',1,'bufsize',200000);
0018
0019 sel = ~strcmp(rxnNames,'');
0020 gpraStrings = gpraStrings(sel);
0021 rxnNames = rxnNames(sel);
0022 subSystems = subSystems(sel);
0023
0024 nRxns = length(rxnNames);
0025 allGenes = {};
0026
0027 h = waitbar(0,'Reading GPRA text file ...');
0028 for i = 1:nRxns
0029 if mod(i,10) == 0
0030 waitbar(i/nRxns,h);
0031 end
0032 thisGpra = gpraStrings{i};
0033 thisGpra = regexprep(thisGpra,'+',' and ');
0034 thisGpra = regexprep(thisGpra,',',' or ');
0035 [thisGenes,rule] = parseBoolean(thisGpra);
0036 genes{i} = thisGenes;
0037 allGenes = [allGenes thisGenes];
0038 rules{i} = rule;
0039 grRules{i} = thisGpra;
0040 end
0041 if ( regexp( version, 'R20') )
0042 close(h);
0043 end
0044
0045 allGenes = unique(allGenes);
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0048 rxnGeneMat = sparse(nRxns,length(allGenes));
0049 h = waitbar(0,'Constructing GPR mapping ...');
0050 for i = 1:nRxns
0051 if mod(i,10) == 0
0052 waitbar(i/nRxns,h);
0053 end
0054 [tmp,geneInd] = ismember(genes{i},allGenes);
0055 rxnGeneMat(i,geneInd) = 1;
0056 for j = 1:length(geneInd)
0057 rules{i} = strrep(rules{i},['x(' num2str(j) ')'],['x(' num2str(geneInd(j)) ')']);
0058 end
0059 end
0060 if ( regexp( version, 'R20') )
0061 close(h);
0062 end
0063
0064 gpraModel.rxns = rxnNames;
0065 gpraModel.genes = columnVector(allGenes);
0066 gpraModel.rules = columnVector(rules);
0067 gpraModel.grRules = grRules;
0068 gpraModel.subSystems = subSystems;
0069 gpraModel.rxnGeneMat = rxnGeneMat;
0070
0071 if (nargin > 1)
0072 [hasGpra,gpraMap] = ismember(model.rxns,gpraModel.rxns);
0073 model.genes = columnVector(gpraModel.genes);
0074 nRxns = length(model.rxns);
0075 nGenes = length(gpraModel.genes);
0076 model.rxnGeneMat = sparse(nRxns,nGenes);
0077 for i = 1:length(model.rxns)
0078 if (hasGpra(i))
0079 gpraID = gpraMap(i);
0080 model.rules{i} = gpraModel.rules{gpraID};
0081 model.rxnGeneMat(i,:) = gpraModel.rxnGeneMat(gpraID,:);
0082 model.subSystems{i} = gpraModel.subSystems{gpraID};
0083 model.grRules{i} = gpraModel.grRules{gpraID};
0084 else
0085 model.rules{i} = '';
0086 model.subSystems{i} = '';
0087 model.grRules{i} = '';
0088 end
0089 end
0090 model.rules = columnVector(model.rules);
0091 model.subSystems = columnVector(model.subSystems);
0092 model.grRules = columnVector(model.grRules);
0093 gpraModel = model;
0094 end
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