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Debug function 'createDummyModel' #2457

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Merged
merged 2 commits into from
Apr 1, 2025
Merged

Debug function 'createDummyModel' #2457

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49b8066
Fixed bug where the S matrix changed after generating createDummyModel
Yanjun2021 Mar 7, 2025
57e9ad5
Fixed bug where the S matrix changed after generating createDummyModel
Yanjun2021 Mar 7, 2025
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12 changes: 9 additions & 3 deletions src/dataIntegration/XomicsToModel/oneRxnPerActiveGene/createDummyModel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -37,13 +37,17 @@
end


if isequal(modelExtractionAlgorithm, 'fastCore') && 0
if isequal(modelExtractionAlgorithm, 'fastCore') %&& 0
paramConsistency.epsilon = fluxEpsilon;
paramConsistency.method = 'fastcc';
[fluxConsistentMetBoolOrig, fluxConsistentRxnBoolOrig] = findFluxConsistentSubset(model, paramConsistency, 2);
if any(~fluxConsistentMetBoolOrig) || any(~fluxConsistentRxnBoolOrig)
warning('%6u\t%6u\t%s\n', nnz(~fluxConsistentMetBoolOrig), nnz(~fluxConsistentRxnBoolOrig),' flux inconsistent metabolites and reactions in input model.')
end

[~, ~, ~, ~, ~, ~, model, stoichConsistModel] = findStoichConsistentSubset(model, ...
0, 0, [], 1e-6 * 10);

end

%any zero rows or columns are considered inconsistent
Expand Down Expand Up @@ -344,14 +348,16 @@
end

if any(~fluxConsistentMetBool) || any(~fluxConsistentRxnBool)

fluxInConsistentRxn = model.rxns(~fluxConsistentRxnBool);
fprintf('%s\n',[int2str(nnz(~fluxConsistentRxnBool)) ' flux inconsistent reaction(s) after dummy model creation, removed:'])
disp(model.rxns(~fluxConsistentRxnBool))

fluxConsistentRxnBool(~fluxConsistentRxnBool ) = 0;

model.S = model.S(fluxConsistentMetBool,fluxConsistentRxnBool);
model.b = model.b(fluxConsistentMetBool,1);
model.csense = model.csense(fluxConsistentMetBool,1);
model.mets = model.mets(fluxConsistentMetBool);
model.rxns = model.rxns(fluxConsistentRxnBool);
model.rxnNames = model.rxnNames(fluxConsistentRxnBool);
model.lb = model.lb(fluxConsistentRxnBool);
Expand Down