Skip to main content

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


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

go-stats-1.1.3.tar.gz (22.2 kB view hashes)

Uploaded source

Built Distribution

go_stats-1.1.3-py3-none-any.whl (25.3 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page