ieugwaspy 1.0.5

Python interface to IEU GWAS database API

Perform fast queries in Python against a massive database of complete GWAS summary data

The IEU OpenGWAS database comprises over 50,000 curated, QC'd and harmonised complete GWAS summary datasets and can be queried using an API. See here for documentation on the API itself. This Python package is a wrapper to make generic calls to the API, plus convenience functions for specific queries.

See ieugwaspy documentation for details of how to use this package.

Installation

Install using pip install ieugwaspy

Features

• Get meta data about specific or all studies
• Obtain the top hits (with on the fly clumping as an option) from each of the GWAS datasets. Clumping and significance thresholds can be specified
• Obtain the summary results of specific variants across specific studies. LD-proxy lookups are performed automatically if a specific variant is absent from a study
• Perform PheWAS (look up all associations for a variant)
• Convert between chromosome:position and rsids and getting annotations

Developer notes

To run tests, use pytest -v -s --select-api="dev"

To generate docs, use pdoc --html ieugwaspy; rm -rf docs/; mkdir docs; mv html/ieugwaspy/* docs/; rm -r html/