RemoveRxns does not always update model fields correctly

[stefaniamagg]

I am working on a test for "removeDeadEnds", and found that the function "removeRxn" does not update the S-matrix correctly in the sample model ("DeadEndTestModel.mat"). I think this has to do with the function "removeFieldEntriesForType". @tpfau , you might know if this can be the case?

My guess is that this also has to do with the sizes of the original and reduced models. The original model has 12 metabolites and 17 reactions, then in the test 3 metabolites and 5 reactions are removed, leaving 9 metabolites and 12 reactions. The function works fine when performed on a model with different dimensions, e.g., the E. coli core model.

>> load('DeadEndTestModel.mat')
>> rxnsRem = findRxnsFromMets(model, model.mets([5; 9; 12])); %rxns that include the dead-end metabolites 5, 9, 12
>> modelRem = removeRxns(model, rxnsRem);
>> length(modelRem.mets)
ans =

     9

>> length(modelRem.rxns)
ans =

    12

>> size(modelRem.S)
ans =

    12    12

I hereby confirm that I have:

• [] Tried to solve the issue on my own
• [X] Retried to run my code with the latest version of The COBRA Toolbox
• [X] Checked that a similar issue has not already been opened

(Note: You may replace [] with [X] to check the box)

[tpfau]

Thanks for pointing this out. This is an stemming from both removeFieldEntriesForType and getModelFieldsForType. The latter doesn't properly check which dimension to remove, the former doesn't return S as both dimensions were matching, as I originally assumed, that this "should not happen" (well, I shouldn't assume stuff...). I'm currently testing a fix for it. and will create a PR as soon as I get it working.

[laurentheirendt]

Thanks @stefaniamagg and @tpfau for fixing this! :+1: