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fix: ignore conflicting grRules and display additional warning #92

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fix: ignore conflicting grRules and display additional warning #92

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24 changes: 14 additions & 10 deletions ecHumanGEM/scripts/preprocessModel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -23,17 +23,21 @@
name = [];
end
end
model = removeFields(model);
[grRules, rxnGeneMat] = standardizeGrRules(model);
model.grRules = grRules;
model.rxnGeneMat = rxnGeneMat;
model = removeFields(model);
%find conflicting grRules in model
[~,~,conflicts] = standardizeGrRules(model);
if ~isempty(conflicts)
warning(sprintf('\nConflicting grRules where found for several reactions (check the above lines). GECKO will ignore these grRules to avoid introduction of potentially wrong enzyme constrains for such cases. It is recommended to check your original GEM and fix these grRules manually with the guidance provided by the function "standardizeGrRules.m" in the RAVEN toolbox.\n'))
end
%delete conflicting grRules to avoid weird enzyme constraints
model.grRules(conflicts) = {''};
%Remove gene rules from pseudoreactions (if any):
for i = 1:length(model.rxns)
if endsWith(model.rxnNames{i},' pseudoreaction')
model.grRules{i} = '';
model.rxnGeneMat(i,:) = zeros(1,length(model.genes));
end
end
pseudoRxns = endsWith(model.rxnNames,' pseudoreaction');
model.grRules(pseudoRxns) = {''};
%standardize grRules
[grRules,rxnGeneMat] = standardizeGrRules(model);
model.grRules = grRules;
model.rxnGeneMat = rxnGeneMat;
% Standardizes the metabolites names
model = modifyMetNames(model);

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