draeger-lab / refinegems

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
https://refinegems.readthedocs.io/en/latest/
MIT License
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Hot fix for polish #95

Closed GwennyGit closed 1 year ago

GwennyGit commented 1 year ago

Describe the bug

Expected behavior

GwennyGit commented 1 year ago

I changed the implementation of how BioCyc identifiers are treated. The newer version makes more sense with the new setup. However, I also found that the 'bug' was not caused by the 'polish' module itself but rather by the fact that in the AGORA 2 models, it was tested on, the BioCyc identifiers contain no indication for the BioCyc sub-database like 'META:' for the MetaCyc database. I think this issue can be coped with in Polish and, thus, before releasing the newer version I will try to cope with missing sub-database prefixes for BioCyc identifiers.

GwennyGit commented 1 year ago

I found another bug within polish concerning the resulting invalid_curies.tsv file. For a lot of entities None values for the database prefix and the corresponding identifier are printed. Before pushing the changes to main and generating a new release I will investigate and fix this bug.