go-stats python tool

Generate statistics for a GO release based on a GOLr instance

Install

pip install go-stats

Content

This package contains several scripts used to compute both statistics and changes of Gene Ontology releases.

• go_stats.py: compute the stats for a given release
• go_ontology_changes.py: compute the changes for two releases (using OBO files)
• go_annotation_changes.py: compute the changes for two releases (using 1 GOLr instance and previously computed stats)
• go_refine_stats.py: used to compute the first stats, including ontology stats
• go_reports.py: used to compute all stats and changes between two releases

Usage

import go_stats

release_date = '2019-09-01'
include_protein_binding = False

json_stats = go_stats.compute_stats('http://golr-aux.geneontology.io/solr/', release_date, include_protein_binding)
go_stats.write_json("stats.json", json_stats)

tsv_stats = go_stats.create_text_report(json_stats)
go_stats.write_text("stats.tsv", tsv_stats)

json_meta = go_stats.create_meta(json_stats)
go_stats.write_json("meta.json", json_meta)

Notes

• current GOLr instance is http://golr-aux.geneontology.io/solr/
• older GOLr archives are stored in zenodo both as full archive and reference archive which can be used with bdbags to retrieve only the golr database dump (golr-index-contents.tgz)
• several scripts will be refactored and simplified (e.g. go_refine_stats.py is used to compute the first set of stats files, then for the next releases one can use go_reports.py)