Convert RECON .mat file to .sbml

[C b]

Hi everyone,

My goal is to obtain a R graph object from RECON3 resources. My plan is to use COBRApy to convert the .mat file from RECON into a sbml file, and then use a R package that converts .sbml to R graph.

I have a virtual env, python 3.8.2, using Jupyter Notebook. Here is my code : 

from cobra.io import load_matlab_model, write_sbml_model

recon = load_matlab_model(".../Recon3D_301.mat")

Here is where I get the error : 

write_sbml_model(recon, "recon3d.xml")

Gives me this : 

LibSBML error code -3: The requested action could not be performed. This can occur in a variety of contexts, such as passing a null object as a parameter in a situation where it does not make sense to permit a null object.

Anyone can help me with this simple task ? I don't get it.
Thank you

[Moritz Beber]

Hello,

Are you the same person who opened https://github.com/opencobra/cobrapy/issues/1104 ? Did that solve your problem?

Best regards,

Moritz

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