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)
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