dnaerys 0.2.0

Python client library for the Dnaerys genome variant store

Dnaerys Python Client

Python client library for Dnaerys, a high-performance distributed genome variant database. Dnaerys stores indexed variant and sample data for large cohorts and serves queries with millisecond latency, including VEP annotations, allele frequencies, and pathogenicity predictions. This library wraps the gRPC API into Pythonic methods with streaming iteration, pagination, and frozen dataclass results. It is designed for bioinformaticians and data scientists working with cohort-scale genomic data.

Full documentation: dnaerys-python.readthedocs.io

Requirements

Python 3.12 or later.

Installation

pip install dnaerys
pip install dnaerys[pandas]   # for to_dataframe() support

Quick Start

from dnaerys import (
    DnaerysClient, Region, AnnotationFilter, Consequence, Impact,
)

tp53 = Region("chr17", 7661779, 7687546)

with DnaerysClient("db.dnaerys.org:443") as client:
    ann = AnnotationFilter(
        impact=[Impact.HIGH, Impact.MODERATE],
        consequence=[Consequence.MISSENSE_VARIANT],
        clin_significance=["PATHOGENIC", "LIKELY_PATHOGENIC"],
    )

    stream = client.select_variants(
        region=tp53,
        annotations=ann,
        limit=10,
    )

    for variant in stream:
        print(variant)

    # Check response metadata
    print(f"Elapsed: {stream.metadata.elapsed_ms}ms")

Features

• Streaming iteration — variant results arrive as lazy iterators with constant memory usage.
• Pagination — paginate_* methods serve fixed-size pages with transparent buffer refills.
• Annotation filtering — filter by VEP annotations, AF, CADD, AlphaMissense, PolyPhen, SIFT, ClinVar significance, and more.
• Inheritance queries — detect de novo, heterozygous dominant, and homozygous recessive variants across trios.
• Kinship analysis — KING-based kinship estimation for cohorts, duos, trios, and external samples.
• Frozen dataclasses — all result types are immutable, slotted, and hashable; safe to cache, copy, and use as dict keys.
• Clean exception hierarchy — gRPC status codes map to specific exception classes with is_retryable flags.
• pandas integration — call to_dataframe() on any variant stream to get a DataFrame.

Documentation

Full documentation including API reference, pagination guide, annotation filter reference, and connection options is available at dnaerys-python.readthedocs.io. The API reference covers all 27 public methods on DnaerysClient.

License

Apache License 2.0 — see LICENSE for details.

Contributing

Contributions are welcome. Please open an issue to discuss proposed changes before submitting a pull request. Bug reports and feature requests can be filed at github.com/dnaerys/dnaerys-python/issues.