Package for converting between genome build coordinates
Project description
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]
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liftover-1.0.1.tar.gz
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