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Python Library to generate statistics on a Gene Ontology (GO) release

Project description

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)

Project details


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