Bug detected in getSubsetEcModel

[mihai-sysbio]

Description of the bug:

Initially spotted here, running the last step of the light tutorial triggers an error.

Reproducing these results:

>> ecHT29 = getSubsetEcModel(ecModel,HT29);
Matrix index is out of range for deletion.

Error in removeReactions (line 41)
        reducedModel.rxns(indexesToDelete)=[];

Error in getSubsetEcModel (line 53)
smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);

System information

• Operating system: macOS 13
• MATLAB version: 2021b
• GECKO version: develop

I hereby confirm that I have:

• Tested my code with all requirements for running GECKO
• Done this analysis in the develop branch of the repository
• Checked that a similar issue does not exist already

[mihai-sysbio]

These two lines are identical

GECKO/src/geckomat/utilities/getSubsetEcModel.m

Line 41 in 38b6768

smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);

GECKO/src/geckomat/utilities/getSubsetEcModel.m

Line 53 in 38b6768

smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);

but I don't understand how come there is no

smallEcModel = removeReactions(bigEcModel,~keepRxns, true, true, true);

[edkerk]

These two lines are identical

GECKO/src/geckomat/utilities/getSubsetEcModel.m

Line 41 in 38b6768

smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);

GECKO/src/geckomat/utilities/getSubsetEcModel.m

Line 53 in 38b6768

smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);

Line 53 should be deleted.

but I don't understand how come there is no

smallEcModel = removeReactions(bigEcModel,~keepRxns, true, true, true);

That would not make sense. The smallEcModel is starting to get generated in line 26, and then modified in the rest of the function.

GECKO/src/geckomat/utilities/getSubsetEcModel.m

Line 26 in 38b6768

smallEcModel = removeGenes(bigEcModel,genesToRemove,true,true,false);

[edkerk]

Resolved in #331