liftover

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', one_based=True)
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', one_based=True)
converter[chrom][pos]

# you can also specify an alternative website to load chain files from
converter = get_lifter('hg19', 'hg38', chain_server='https://www.example.com')

# this also matches the core pyliftover interface
from liftover import LiftOver # synonym for `get_lifter`

lifter = LiftOver('hg19', 'hg38') # or LiftOver(PATH_TO_CHAIN), but not LiftOver(filehandle)
lifter.convert_coordinate(chrom, pos)

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