pytrate

Inferring effects of amino acid changes on antigenic phenotypes of viruses.

See the docs.

Install

uv pip install git+https://github.com/davipatti/pytrate.git

Main features

• SeqDf — aligned amino acid sequence management
• CrossedSiteAaModel — Bayesian model with crossed site and amino acid pair effects
• CombinedSiteAaModel — Bayesian model with combined site-amino acid effects
• FoldChangeModel — decompose titer fold changes from mutant vs root viruses
• MapCoordModel — Bayesian antigenic map natural experiments and visualization

Tests

uv run --extra dev pytest

Some tests are a bit slow, do uv run --extra dev pytest -k 'not slow' to skip them.

Build & publish

uv sync --extra dev
uv run python -m build
uv run python -m twine upload dist/*

Pre-commit hook

To enable the pre-commit hook, symlink it into your local .git/hooks directory:

ln -s hooks/pre-commit .git/hooks/pre-commit