https://github.com/jeremymcrae/liftover

liftover for python, made fast with cython
https://github.com/jeremymcrae/liftover

cython liftover python

Last synced: 3 months ago
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liftover for python, made fast with cython

• Host: GitHub
• URL: https://github.com/jeremymcrae/liftover
• Owner: jeremymcrae
• License: mit
• Created: 2019-02-15T18:41:18.000Z (over 7 years ago)
• Default Branch: main
• Last Pushed: 2026-04-18T01:37:20.000Z (3 months ago)
• Last Synced: 2026-04-18T03:04:48.101Z (3 months ago)
• Topics: cython, liftover, python
• Language: Python
• Homepage:
• Size: 1.37 MB
• Stars: 98
• Watchers: 1
• Forks: 6
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
![liftover](https://github.com/jeremymcrae/liftover/workflows/liftover/badge.svg)

### python liftover utility

Converts point coordinates between genome assemblies.

Inspired by [pyliftover](https://github.com/konstantint/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

```python

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)

```