Hot fix for gapfill - Githubissues

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 gapfill #76

Closed GwennyGit closed 1 year ago

GwennyGit commented 1 year ago

Describe the bug

In the user command line interface to generate a config.yaml file selecting n for Do you want to use functions to modify your model? an error occurs that the key 'gapfill_model' does not exist.
In gap_analysis the functions to retrieve the chemical formulae as well as the charges for metabolites from ChEBI does cause an error due to being cast to int.

Solution

[x] Add user_input['gapfill_model'] = False after line 509 in io
[x] Adjust cast to int for ChEBI IDs in analysis_biocyc and gapfill to also handle NaN

GwennyGit commented 1 year ago

I am still testing if it works but on a minimal example the adjustments already worked.