Metadata-Version: 2.1
Name: go-stats
Version: 1.1.3
Summary: Python Library to generate statistics on a Gene Ontology (GO) release
Home-page: https://github.com/geneontology/go-stats
Author: Laurent-Philippe Albou
Author-email: laurent.albou@lbl.gov
License: UNKNOWN
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/](http://golr-aux.geneontology.io/solr/)
        * older GOLr archives are stored in zenodo both as [full archive](https://zenodo.org/record/3267438#.XXN5spNKg4M) and [reference archive](https://zenodo.org/record/3267437#.XXN5spNKg4M) which can be used with [bdbags](https://geneontology.github.io/docs/tools-guide/#programmatic-download-bdbag) 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)
Keywords: GO,Gene Ontology,annotation,ontology,stats,changes,GOLR,statistics
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: BSD License
Description-Content-Type: text/markdown
