Comments (4)
@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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Related Issues (20)
- help: randomSampling with human-GEM HOT 10
- changeGeneAssoc not work if all the gene already are in the model
- bug: on Apple silicon CPU getDiamond fails HOT 4
- Failed to make blastp executable HOT 4
- fix: addRxns definition of `rev` field
- chore: update tINIT references HOT 3
- solveLP() does not work because of issue in code HOT 6
- RAVEN >= v2.7.7 getModelFromHomology generates invalid GPRs from Recon3D HOT 3
- Error: ftINIT - failed to find good enough solution within time frame HOT 14
- help: getKEGGModelForOrganism gives error when using dispEM HOT 1
- bug: RAVEN 2.8.2 checkInstallation on new install
- bug: model loaded from YAML has no c-field
- bug: soplex reported failure, even when functional
- SBO terms not exported properly to Excel format when they are within MIRIAM annotations HOT 5
- Can fast tINIT integrate data from bulk RNA-seq? HOT 8
- Unrecognized field name "compNames" with ravenCobraWrapper error
- bug: make binaries executable on Ubuntu
- bug: simplifyModel with irreversible backwards-only reactions
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