bug: fillGaps errors when using KEGG as template model about raven HOT 4 CLOSED

@phemmy2k2 thanks for the detailed information. In the last command, you haven't specified params. This is not required, so I ran it without specifying the 'params' parameter: [newConnected, cannotConnect, addedRxns, balancedModel, exitFlag]=fillGaps(CombinedDraftModel,keggModel,true,false,false,[]);

When I run this with the latest RAVEN (2.0.1), I don't get the same error message as you get. Are you sure you use the latest RAVEN release?

However, I did stumble upon another issue if you use the "whole KEGG model", obtained with keggModel=getModelFromKEGG([],false,false,false);, as the reference model. When executed that way, it doesn't construct a grRules structure, as this would be excessively long, including all KEGG genes. So best to get rid of the genes and rxnGeneMat fields before running fillGaps:

keggModel=rmfield(keggModel,'genes')
keggModel=rmfield(keggModel,'rxnGeneMat')

I've added a note mentioning this in the getModelFromKEGG function: 99d2146

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Thank you @edkerk I have it running with version 2.0.1. However, I discovered that getKEGGModelForOrganism() is throwing error in the latest version. Below is the code and the error, you can try to replicate it.

model_KEGG=getKEGGModelForOrganism('dme',false,false,false);
Error using exist
The first input to exist must be a string scalar or character vector.

Error in getKEGGModelForOrganism (line 221)
if ~(exist(fastaFile,'file')==2)

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You're not providing all parameters that are required (in MATLAB you cannot just skip parameter values for function inputs). If you run help getKEGGModelForOrganism, you'll see that the third parameter should be fastaFile, which should be a string, and if you don't want to provide a fasta file you still need to provide an empty string: ''. The third option is dataDir, again this is optional, but if you don't want to supply it, it should again be an empty string: ''. Etc, etc.

What you're probably trying to do here works with the following command:

model_KEGG=getKEGGModelForOrganism('dme','','','',false,false,false);

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Documentation of the functions is amended in version 2.0.2.

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