liftover 1.0.1

Package for converting between genome build coordinates

python liftover utility

Converts point coordinates between genome assemblies. Inspired by pyliftover, the primary advantage this offers is dictionary style conversion, as in access converted coordinates via converter[chrom][pos].

Installation

Install via pip: pip install liftover

Usage

from liftover import get_lifter

converter = get_lifter('hg19', 'hg38')
chrom = '1'
pos = 103786442
converter[chrom][pos]

converter.query(chrom, pos)

# alternatively create a converter directly from a chainfile
from liftover import ChainFile
converter = ChainFile('/home/user/hg18ToHg38.over.chain.gz', 'hg18', 'hg38')
converter[chrom][pos]