Unrecognized field name "compNames" with ravenCobraWrapper error

[PkiwiBird]

Hi,
when trying to convert a raven model to a cobra model with ravenCobraWrapper, I get the following error:

Converting COBRA structure to RAVEN..
Unrecognized field name "compNames".

Error in ravenCobraWrapper (line 216)
        newModel.mets=regexprep(newModel.mets,['\[', model.compNames{i}, '\]$'],'');

Do you have any idea on how to solve this?

[edkerk]

How did you load this RAVEN model (with what command)? And would you be able to link to its source (where did you get the model from)?

[PkiwiBird]

It was solved by using compNames and comps as fields but now there's another problem.

The model is a liver model extracted from the complete body model. Inside Dataset EV1 there is the male whole body model: MSB-16-e8982-s022/PSCM_toolbox/SuppliedResults/OrganAtlas_Harvey.mat.
The following code is used to extract the liver model and save as .yml:

load 'OrganAtlas_Harvey.mat'
omc_ml=OrganCompendium_male; % organ model compendium of male
liver_ml=omc_ml.Liver.modelAllComp; % liver model of male
compNames = {'cytosol'; 'lysosome'; 'mitochondria'; 'endoplasmatic reticulum';
'golgi apparatus'; 'peroxisome'; 'nucleus'; 'inner mitochondria space';
'bile duct liver'; 'blood portal vein liver'; 'blood portal vein';
'blood circulation'; 'bile duct'};
comps = {'c'; 'l'; 'm'; 'r'; 'g'; 'x'; 'n'; 'i'; 'bdL'; 'bpL'; 'bp'; 'bc'; 'bd'};
liver_ml.compNames = compNames;
liver_ml.comps = comps;
liver_ml = ravenCobraWrapper(liver_ml);
writeYAMLmodel(liver_ml, fullfile(BaseDir,'results', 'liver_ml_GEM.yml'));

The last command gives the error:

Brace indexing is not supported for variables of this type.

Error in writeYAMLmodel>writeField (line 276)
                    list{j} = ['"' list{j} '"'];

Error in writeYAMLmodel (line 100)
    writeField(model, fid, 'subSystems',           'txt', i, '  - subsystem',             preserveQuotes)

Could you help point in the right direction, please?

[edkerk]

First, in your original post you mention

convert a RAVEN model to a COBRA model

but the model is already in COBRA format.

But if you meant to write "COBRA to RAVEN model", then:

1. Do not define the comps and compNames fields as done above, you'd want ravenCobraWrapper to define them and appropriately refer to them in metComps.
2. After ravenCobraWrapper is finished, manually corrected the entries in liver_ml.compNames, as they will by default be the same abbreviations as in .comps.
3. To deal with the above and the odd mixture of nested cell arrays that are used for the subSystems field, I've made some changes to ravenCobraWrapper and readYAMLmodel.

So first get these two functions from PR #522, and then run:

load 'OrganAtlas_Harvey.mat'
omc_ml=OrganCompendium_male; % organ model compendium of male
liver_ml=omc_ml.Liver.modelAllComp; % liver model of male
liver_ml = ravenCobraWrapper(liver_ml);
%% Manually curate the liver_ml.compNames field before continuing
writeYAMLmodel(liver_ml, fullfile(BaseDir,'results', 'liver_ml_GEM.yml'));

[edkerk]

This is now also turned into issue #523

[PkiwiBird]

Thank you very much!