GA4GH VRS and VRSATILE Pydantic Models

0.2.0 verified Sat May 09 auth: no python

Provides Pydantic data models for the GA4GH Variation Representation Specification (VRS) and VRSATILE schemas. Currently at v0.2.0, this library transitioned from Pydantic v1 to v2 in a major breaking change. Active development with experimental pre-releases.

pip install ga4gh-vrsatile-pydantic

Common errors

error ga4gh.vrsatile.pydantic doesn't exist ↓

cause Version mismatch: code assumes Pydantic v1 import path (pre-0.2.0) or uses wrong submodule.

fix

Install ga4gh-vrsatile-pydantic>=0.2.0 and ensure imports are from ga4gh.vrsatile.pydantic.

error AttributeError: 'Allele' object has no attribute 'dict' ↓

cause Code written for Pydantic v1 (.dict()) but using v0.2.0 which uses Pydantic v2 (.model_dump()).

fix

Replace .dict() with .model_dump() and .json() with .model_dump_json().

Warnings

breaking v0.2.0 migrated from Pydantic v1 to v2. All .dict() calls must be replaced with .model_dump(), and .json() with .model_dump_json(). ↓

fix Replace all .dict() with .model_dump() and .json() with .model_dump_json() in your code.

deprecated v0.1.0-dev releases (pre-release) used Pydantic v1. These are not compatible with v0.2.0. Avoid using dev versions in production. ↓

fix Upgrade to v0.2.0 and migrate code to Pydantic v2 syntax.

gotcha The import path changed after v0.2.0. Models were previously under ga4gh.vrsatile.models but now under ga4gh.vrsatile.pydantic. ↓

fix Update imports: from ga4gh.vrsatile.pydantic import Allele (instead of from ga4gh.vrsatile.models import Allele).

Imports

Allele

wrong

from ga4gh.vrsatile.models import Allele

correct

from ga4gh.vrsatile.pydantic import Allele

Pre-v0.2.0 import path changed after migration to pydantic v2

CopyNumberChange

wrong

from ga4gh.vrsatile.pydantic.vrsatile_models import CopyNumberChange

correct

from ga4gh.vrsatile.pydantic import CopyNumberChange

Incorrect submodule path – models are exported directly from pydantic module

Quickstart

Creates a VRS Allele model using Pydantic v2 syntax.

from ga4gh.vrsatile.pydantic import Allele, CopyNumberChange

# Example: creating an Allele
allele = Allele(
    type="Allele",
    location={
        "type": "SequenceLocation",
        "sequence_id": "ga4gh:SQ._0wi-qoPhFdH",
        "interval": {
            "type": "SequenceInterval",
            "start": {"type": "Number", "value": 55181320},
            "end": {"type": "Number", "value": 55181321}
        }
    },
    state={
        "type": "LiteralSequenceExpression",
        "sequence": "A"
    }
)

# Validate
print(allele.model_dump_json(exclude_none=True))