uniprotlib

Note: This library was vibe coded with Claude. It works, it's tested, but review accordingly.

Python library for parsing UniProt XML files. Handles both single-entry downloads and multi-GB gzip-compressed database dumps with bounded memory usage.

Installation

pip install uniprotlib

Or with uv:

uv add uniprotlib

Usage

from uniprotlib import parse_xml

# single file
for entry in parse_xml("Q9Y261.xml"):
    print(entry.primary_accession, entry.protein_name)

# gzipped bulk download
for entry in parse_xml("uniprot_sprot.xml.gz"):
    print(entry.gene.primary, entry.organism.scientific_name)

# multiple files
for entry in parse_xml("human.xml.gz", "mouse.xml.gz"):
    print(entry.primary_accession)

parse_xml() returns an iterator that yields UniProtEntry objects. Gzip detection is automatic based on the .gz extension. Memory stays bounded regardless of file size.

Parsed fields

All model classes are dataclasses with full type annotations and py.typed support.

Development

Requires Python >= 3.12 and uv.

uv sync
uv run pytest tests/ -v

License

MIT