Ensembl VEP

Ensembl VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.

NOTE: This project is in an initial development phase. Many features are incomplete, APIs may change without notice, and documentation is partial. Use at your own risk and feel free to open issues or contribute; your feedback is welcome.

Documentation

Full documentation is available at: https://ensembl.github.io/ensembl-vep-py/

Installation

Requirements

• Python 3.12 or higher
• Rust 1.95.0 or higher (TBD - not strictly tested)
• Dependencies listed in pyproject.toml and Cargo.toml

Using pip (TBD - after PyPI release)

pip install ensembl-vep

Using uv (recommended) (TBD - after PyPI release)

uv pip install ensembl-vep

Development Installation

1. clone the repository

   git clone https://github.com/Ensembl/ensembl-vep-py.git
   cd ensembl-vep-py

2. Create a branch against remote main branch

   git checkout -b feature/some_feature origin/main

3. Install the package in editable mode

   uv pip install -e .

See more details in the Contributing Guide guide.

Quick Start

Basic Usage

from ensembl_vep import hello

print(hello("world!"))

Command-Line Interface

vep world!

Configuration

Cache Files (TBD)

Testing

Run the test suite:

# Run pytest with coverage
uv run coverage run -m pytest

# Run Rust llvm-cov
cargo llvm-cov --ignore-filename-regex '(^|/)src/rust/lib\.rs$'

The Rust crate root src/rust/lib.rs is reserved for PyO3 module registration glue. Keep testable Rust logic in submodules; coverage runs ignore lib.rs so the project can use stable Rust without nightly-only coverage attributes.

Contributing

We welcome contributions! Please see our Contributing Guide for details.

Citation (TBD)

If you use this software, please cite:

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.
The Ensembl Variant Effect Predictor.
Genome Biology Jun 6;17(1):122. (2016)
doi:10.1186/s13059-016-0974-4

Support (TBD)

• Bugs: Issues
• Features: Discussions → Ideas

Changelog (TBD)

See CHANGELOG.md for version history and updates.

Acknowledgments (TBD)