UniProtPy

A Python library that interfaces with UniProt.

For something like openvax/pyensembl with UniProt.

The REST API has changed as of 2022. Many of the ways to extract data from UniProt is now different and there isn't a clean way to interface with the new API. This library aims to provide a clean interface to access all protein data from UniProt.

Goals

1. Allow users to pull any kind of data from UniProt.
2. Store and query large data using a local database.
3. Manipulate and output data in many standard formats.

Installation

pip install uniprotpy

Getting a proteome by proteome ID

uniprotpy get-proteome --proteome_id UP000005640

Getting the best proteome for a taxon ID

uniprotpy get-best-proteome --taxon_id 9606

TODO

• Retrieve individual entries in all supported formats.
• Get metadata (protein ID, name, gene, # of isoforms, etc.) for entries.
• Retrieve proteomes via proteome ID or select "best" proteome based on taxon ID.
• Query proteomes for a protein by ID, name, seq, or peptide unit.