Metadata-Version: 2.5
Name: altar-alphagenome
Version: 0.2.0
Summary: AlphaGenome hosted-API model binding for inline Altar variant scoring
Project-URL: Documentation, https://kundajelab.github.io/altar/
Author: Riya Sinha
License-Expression: MIT
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Python: >=3.12
Requires-Dist: alphagenome==0.9.0
Requires-Dist: altar<0.3,>=0.2.0
Provides-Extra: test
Requires-Dist: pytest-asyncio>=0.24; extra == 'test'
Requires-Dist: pytest>=8; extra == 'test'
Description-Content-Type: text/markdown

# Altar AlphaGenome binding

> [!WARNING]
> The default prioritization rule is an explicitly untuned placeholder. Calibrate it for your cohort and
> question before relying on it.

`altar-alphagenome` connects Google DeepMind's hosted [AlphaGenome](https://github.com/google-deepmind/alphagenome)
API to Altar. It registers `ALPHAGENOME` in Altar's canonical `altar.model_plugins` group and scores inline:
`build_scoring_plan` returns a JSON-durable `InlineScoringPlan`, and `execute_inline` calls the API in process
without an execution backend or container.

The binding is not on PyPI. Install it from a clone of the repository, which also installs Altar from the same
checkout:

```bash
uv pip install -e bindings/alphagenome
```

The binding depends on the exact `alphagenome` SDK release recorded in its runtime identity and refuses to
execute with a different version. The SDK is imported only when the default scorer runs, so plans can be built,
validated, and materialized without loading the client.

An Altar model instance is AlphaGenome plus its configured organism, ontology terms, variant scorers, and
sequence length. The binding always calls the production `ALL_FOLDS` model rather than exposing training folds
in user configuration. Human coordinates must be hg38 and mouse coordinates mm10. The API key is a
`SecretReference` in durable configuration; the raw key, an injected scorer, or an SDK client reaches the
plugin only through the non-durable `AlphaGenomeRuntime`.

Each variant yields one scalar headline row (`top_output_type`, `top_track`, `max_abs_raw_score`,
`top_track_abs_quantile_score`, `max_abs_quantile_score`, `n_tracks_scored`) and a lossless `track_scores`
detail table with one row per scorer and genomic track. Persist the detail table with any Altar `DetailStore`.

See the [AlphaGenome integration page](https://kundajelab.github.io/altar/integrations/alphagenome/) for the
reduction, prioritization rule, and compatibility notes. API quota, availability, privacy policy, and provider
terms of use apply independently of this MIT-licensed binding.
