liftover 1.1.9

Package for converting between genome build coordinates

python liftover utility

Converts point coordinates between genome assemblies. Inspired by pyliftover, this offers a few advantages:

• ~5X faster, and lower memory requirements, as loading the chain file and converting coordinates is implemented in c++.
• 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]

# other synonyms for the lift call
converter.convert_coordinate(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]