Introduction

UCSC Bed is a module for creating a BED file out of the UCSC refseq genes list. It is able to connect to, download, and process the genes list from the UCSC ftp site for any reference genome.

Installation

Just run pip install ucsc_bed

CLI

Use ucsc_bed REFERENCE --email EMAIL > exons.bed, where REFERENCE is the name of the genome build you want a bed file for (e.g. hg19, hg38 etc.), and EMAIL is your email address that is used when logging onto the UCSC FTP site (you don't require registration)

API

You can also access the bed file in python like this:

import ucsc_bed

bed_str = ucsc_bed.download_table('hg38', 'email@email.com')
print(bed_str)