This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

Variant Effect Prediction for Python

Project Description

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.

Release History

Release History

This version
History Node

0.0.1

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting