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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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changes in analysis_biocyc.py, analysis_db.py, gapfill.py #101

Closed f3rryman closed 11 months ago

f3rryman commented 11 months ago

analysis_biocyc.py:

  1. chemical formula error catching
  2. check if input paths exists because PICNIC

analysis_db:

  1. added multiprocessing for BiGG db requests, currently splitted in 5 threads, more might overwhelm db?

  2. TODO: progress bar is not working

  3. TODO: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_index,col_indexer] = value instead in line 165, 170 -> however .loc is used, I dont see the issue here...

gapfill.py:

  1. avoid conflicts while converting None ChEBI values to floats
GwennyGit commented 11 months ago

analysis_biocyc.py & gapfill.py can be merged into dev. analysis_db.py could also be merged as point 3 is not necessarily to be fixed, but we could add at the top of the file under the import of pandas: pd.options.mode.chained_assignment = None. For point 2, if we cannot add a progress bar, we should print for now how long the process might take under the printout when the process is started.

@f3rryman If you add the changes today, I can integrate them into the new release. We could add a working progress bar in a later release also for analysis_db.py point 3.

f3rryman commented 11 months ago

Fixed the progress bar bug & added the pd.options.mode.chained_assignment = None line to _analysisdb.py