Precomputed db

[ArnaudBelcour]

Add

• New command esmecata_create_db to create database from different output folders of esmecata (from_runs).
• Full release of esmecata precomputed associated with the first version of esmecata precomputed database.
• Option threshold (-t) to precomputed.
• Add --gseapyCutOff option to gseapy_enrichr.
• A check after database creation to detect taxon with few predicted proteins compared to higher affiliated taxon.
• Check the good format of the gzip file.
• Header KEGG_reaction in annotation_reference from annotation_uniprot to avoid issues with esmecata_create_db.

Fix

• Issue with protein IDs from UniParc during annotation (incorrect split on '|').
• Fix issue in get_taxon_obs_name function.
• Issues in test.

Modify

• Add database version in log.
• Rename test_workflow.py into test_workflow_uniprot.py, to better reflect what is done.
• Update workflow figure.
• Update readme.
• Update article_data folder and the associated readme.