RAVEN >= v2.7.7 getModelFromHomology generates invalid GPRs from Recon3D #481
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fixed in develop
This issue is fixed and pushed to develop branch. Will be closed when fix appears in master branch.
Description of the issue:
I've previously used RAVEN v2.7.6 to extract GEMs using latest Recon3D version as the single template model. Usually, my next steps are to then export the
.mat
object with the new model, load it intoCOBRApy
(cobra.io.load_matlab_model()
) and export as a SBML file for further use. This all would go fine.With the Recon3D as my template, I would get this warning about GPRs:
Now I have moved to v2.8.0, and have tried to run the model generation pipeline again. I get the same warning about GPRs, and then COBRApy fails to parse some of the GPRs, reporting an unexpected EOF:
(times 300 or so)
Reading the changelog, I thought this has to do with the removal of
OLD_
genes from the GPRs ingetModelFromHomology
(3rd fix in the log). So I have tested the same script again on v2.7.6 and v2.7.7. Indeed, v2.7.6 works fine, and v2.7.7-generated models have invalid GPRs. RAVENexportModel()
call with an SBML-format file as output also gets stuck on v2.7.7-generated models.System information
*** THE RAVEN TOOLBOX ***
=== Model import and export ===
=== Model solvers ===
=== Essential binary executables ===
=== Compatibility ===
*** checkInstallation complete ***
I hereby confirm that I have:
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