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

Model	Fields
UniProtEntry	primary_accession, accessions, entry_name, dataset, protein_name, gene, organism, sequence, keywords, db_references
Gene	primary, synonyms, ordered_locus_names, orf_names
Organism	scientific_name, common_name, tax_id, lineage
Sequence	value, length, mass, checksum
DbReference	type, id, molecule, properties

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