JGI.py fixes - Githubissues

ELIFE-ASU / ecg

Pulling information from biological databases, and converting it into easy to use gmls for network science.

MIT License

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JGI.py fixes #24

Closed bxk334 closed 4 years ago

bxk334 commented 4 years ago

Plethora of fixes and changes to increase robustness, efficiency, and speed including:

Updated CLI to argparse
Fixed combined_taxon_id.json
Removal of .dat temp files
Reworked tracking of download process with creation and editing of organism url list json file
Only queries JGI for organism list the first time script is run. Checks json and local files thereafter.
Rewrote enzyme url creation
Rewrote metadata and genome statistic dictionary creation

bxk334 commented 4 years ago

Updated documentation/examples for CLI for ecg.py, jgi.py, and kegg.py. Updated CLI to argparse for ecg.py, jgi.py, and kegg.py. Made minor fixes to CLI for jgi.py and kegg.py with respect to passing lists as arguments.