My Utilities

This repository hosts a collection of single-file scripts I wrote that may be useful to people. They are typically written in Python 3, with a simple command-line interface including help information.

list_all_authors.py

Generates a list of authors with their information on the last paper of each author as well as the number of papers co-authored from a Medline-formatted PubMed paper list. Useful for populating the collaborators and other affiliations (COA) table for grant agencies.

refseq_build.py

Sample, download and organize a reference genome database from NCBI RefSeq.

kegg_query.py

Fetch hierarchical mappings and descriptions of a given list of KEGG Orthology (KO) entries from the KEGG server using the official KEGG API.

metacyc_build.py

Extract hierarchical mappings and descriptions from a local copy of the MetaCyc database.

go_build.py

Extract hierarchical mappings and descriptions from the Gene Ontology (GO) database.