Veppy: Variant Effect Prediction for Python

WARNING: This code is an alpha release and not production-ready. APIs may change at any time.

Veppy is a genetic variant effect predictor for Python. Inspired by SnpEff and VEP.

Installation

$ pip install veppy

Installation from source

$ git clone git@github.com:solvebio/veppy.git
$ cd veppy
$ python setup.py install

Setup

Step 1 (OPTIONAL): Prepare a directory for veppy data

The default data path is: ./data

You can override this by setting $VEPPY_DATA_DIR.

export VEPPY_DATA_DIR=/opt/veppy

Step 2: Download source data and build indexes

NOTE: This step downloads about 1gb of data. After indexing, the data directory will consume about 8gb of disk space.

./scripts/download_data_GRCh37.sh

Step 3: Index the source data

python ./run_index.py

Example Usage

>>> from veppy.veppy import calculate_consequences
>>> variant = ('1', 8025384, 'A', 'T')
>>> result = calculate_consequences('GRCh37', *variant)
>>> print result.results

Testing

Tests are currently based on chr1 versions of input data. Full genome tests are coming soon!

$ nosetests

Coverage:

$ nosetests --with-coverage --cover-package=veppy

About SolveBio

SolveBio is a genomics company based in New York City.