coord2gene

Coord2gene is a simple Python script that converts genomic coordinates to gene names. Useful for mapping SNPs to genes, and optimized for speed.

Purpose of Software

This script will read genomic coordinates (chromosome and locus) from an Excel file (xlsx) and look up the gene name using PyEnsembl. Using a local copy of the human genome, it can run very fast (300k+ coordinates in about 10 minutes).

Dependencies

1. Python 3

2. openpyxl

3. PyEnsembl

   • A locally cached copy of a genome, installed using PyEnsembl

Installation

Windows: Currently, this script will not run on Windows due to limitations of 3rd party packages on which it depends.