Error in getINITModel2

[Flash1593]

During the execution of getINITModel2 I'm getting an error:

TNBC_GEM=getINITModel2(refModel, tissue, celltype, hpaData, arrayData, metabolomicsData, removeGenes, taskFile, useScoresForTasks, printReport, taskStructure, params, paramsFT);
***Generating model for: TNBC
-Using array data
-Using metabolic tasks

Reference model statistics:
13069 reactions, 3067 genes
Mean reaction score: 4.2351
Mean gene score: 8.2564
Reactions with positive scores: 54.1817%

Pruned model statistics:
11880 reactions, 2494 genes
Mean reaction score: 4.2651
Mean gene score: 8.0803
Reactions with positive scores: 54.4697%

Reactions essential for tasks:
382 reactions, 364 genes
Mean reaction score: 8.2909
Mean gene score: 8.156
Reactions with positive scores: 86.6492%

MILP detected.
Error using regexprep
All cells must be char row vectors.

Error in optimizeProb>renameparams (line 193)
paramlist = regexprep(paramlist,old{i},new{i});

Error in optimizeProb (line 84)
prob.csense = renameparams(prob.csense, {'L','G','E'}, {'<','>','='});

Error in runINIT (line 312)
res=optimizeProb(prob,params);

Error in getINITModel2 (line 337)
[~, deletedRxnsInINIT, metProduction] = runINIT(simplifyModel(cModel),rxnScores,metabolomicsData,essentialRxnsForTasks,0,true,false,params);

Please see if I'm doing anything incorrect.

[JonathanRob]

Hi @Flash1593, thank you for your patience with this and other issues. This is yet again due to a inconsistency that arose between Human-GEM and RAVEN while adding new features. It should have already been fixed on the develop branch of Human-GEM, so can I ask you to try and clone the develop branch from Human-GEM (instead of main), and see if that solves the problem?

I think Human-GEM is due for a new major release which will merge all the changes/fixes from develop into main, but it won't be immediate.

[Flash1593]

Hi, I tried the Human-GEM from the develop branch.
First the importYaml function gave this error

ihuman = importYaml('Human-GEM.yml');
Start importing...
1
2
3
4
5

importing completed
follow-up processing...Error using getGenesFromGrRules
Too many input arguments.

Error in importYaml (line 271)
[genes, rxnGeneMat] = getGenesFromGrRules(model.grRules, model.genes);

I removed the model.genes from the code & then the import was successful.

checkTasks is also working fine.

But getINITmodel2 is giving the same exact error -

MILP detected.
Error using regexprep
All cells must be char row vectors.

Error in optimizeProb>renameparams (line 193)
paramlist = regexprep(paramlist,old{i},new{i});

Error in optimizeProb (line 84)
prob.csense = renameparams(prob.csense, {'L','G','E'}, {'<','>','='});

Error in runINIT (line 312)
res=optimizeProb(prob,params);

Error in getINITModel2 (line 340)
[~, deletedRxnsInINIT, metProduction] = runINIT(simplifyModel(cModel),rxnScores,metabolomicsData,essentialRxnsForTasks,0,true,false,params);

The problem is in the regexprep function in optimizeProb code. What can I do to rectify the error?

[edkerk]

A new RAVEN version will be released in a few days.

[JonathanRob]

Ok I found the error and have made a PR that fixes the problem.

[JonathanRob]

@Flash1593 in the meantime before the fix is introduced in a new release, you can use this branch of RAVEN to run tINIT.

[Flash1593]

The fix actually worked and tINIT is working fine now. Thanks for the help and support for the problem.

[JonathanRob]

Ok great! In the future, feel free to open an Issue if your problem looks like a bug or you're getting errors or something. Not that it makes much of a difference, but might fit better.