ga4gh-vrs

library2.3.1pypypi✓ verified 85d ago

GA4GH Variation Representation Specification (VRS) reference implementation in Python. Provides data models, validation, and conversion tools for representing genetic variation in a standardized manner. Current stable version is 2.3.1 (Python >=3.10). Pre-releases track VRS 2.1.0 snapshots. Released semi-regularly with bug fixes and feature updates.

data serialization

pip install ga4gh-vrs

github ↗package ↗docs ↗changelog ↗

INSTALL

IMPORT

SIG · GA4GH-VRS

ga4gh-vrs

datapythonv2.3.1

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Allele

✓ from ga4gh.vrs.models import Allele

Primary model class for representing an allele.

VrsObject

✓ from ga4gh.vrs.models import VrsObject

Base class for all VRS objects.

copy_to_toplevel

✓ from ga4gh.vrs.extras import copy_to_toplevel

Utility function to copy VRS objects to top-level.

DataProxy

✓ from ga4gh.vrs.dataproxy import create_dataproxy

✗ from ga4gh.vrs.dataproxy import DataProxy

Use create_dataproxy factory function instead of importing DataProxy directly.

Build a simple VRS Allele using SequenceLocation and LiteralSequenceExpression, using a SeqRepo data proxy.

from ga4gh.vrs.models import Allele from ga4gh.vrs.dataproxy import create_dataproxy # Create a data proxy with optional health check (set disable_healthcheck=True to skip) dp = create_dataproxy('seqrepo', disable_healthcheck=True) # Build an Allele object allele = Allele( location={ "type": "SequenceLocation", "sequence_id": "ga4gh:SQ.IIB53T8CNeJJdUqGN9Kj2b", "interval": {"type": "SimpleInterval", "start": 0, "end": 10} }, state={ "type": "LiteralSequenceExpression", "sequence": "ACGTGCATGT" } ) print(allele.model_dump_json(indent=2))

Debug

Known issues

breakingVersion 2.0 introduced new models (pydantic v2). Existing code using v1.x models will break. Allele, Variation, etc. must be imported from ga4gh.vrs.models.

fix

Update imports and migrate to pydantic v2 model_dump()/model_dump_json() instead of dict()/json().

affects: <2.0

deprecatedBeacon translation function is deprecated since v2.2.0 and may be removed.

fix

Avoid using beacon-related translation utilities; use direct VRS models instead.

affects: >=2.2.0

breakingIn v2.3.0, the health check is removed from VCF annotator and create_dataproxy now has a disable_healthcheck keyword argument. Calling create_dataproxy without it may raise errors if the underlying service is unavailable.

fix

Pass disable_healthcheck=True to create_dataproxy if you don't need health checks.

affects: >=2.3.0

gotchaThe HGVS dependency changed from <1.5 to >=1.5.5,<2.0 in v2.3.0. Pinning to older hgvs breaks installation. Ensure you install with compatible version.

fix

Use 'pip install ga4gh-vrs' which automatically resolves the correct HGVS version.

affects: >=2.3.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'ga4gh.vrs'

Package not installed or installed with wrong name (e.g., 'vrs' instead of 'ga4gh-vrs').

fix

Run 'pip install ga4gh-vrs' and ensure you have Python >=3.10.

ImportError: cannot import name 'Allele' from 'ga4gh.vrs'

The Allele class is no longer directly in ga4gh.vrs; it moved to ga4gh.vrs.models.

fix

Use 'from ga4gh.vrs.models import Allele'.

AttributeError: 'Allele' object has no attribute 'to_dict'

Using pydantic v2 model methods incorrectly. The .dict() method is deprecated.

fix

Use .model_dump() instead of .dict(), and .model_dump_json() instead of .json().

ga4gh.vrs.dataproxy.DataProxyException: Could not connect to SeqRepo

The data proxy health check failed because SeqRepo service is not running or unreachable.

fix

Set disable_healthcheck=True in create_dataproxy() to skip the connection test.

Upgrade

Version history

2.3.1latest on PyPI · released Feb 10, 2026

Audit

Dependencies

ga4gh.vrsatileoptionalVRSATILE standard dependencies for VRS models

hgvsrequiredHGVS parsing and conversion (>=1.5.5,<2.0)

Agent activity

14 hits · last 30 days

node

Resources

githubhttps://github.com/ga4gh/vrs-python ↗

packagehttps://pypi.org/project/ga4gh-vrs/ ↗

docshttps://github.com/ga4gh/vrs-python ↗

changeloghttps://github.com/ga4gh/vrs-python/releases ↗