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]