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)
1 maintainer
Metadata
1 maintainer
Release files for liftover 1.5.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| liftover-1.5.0.tar.gz | 244.5 kB | Details |
Built distributions (wheels)
Total release size: 43.2 MB
Release files / liftover-1.5.0.tar.gz
| Download URL | liftover-1.5.0.tar.gz |
|---|---|
| Size | 244.5 kB |
| Tags | Source |
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twine/7.0.0 CPython/3.13.14
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Release files / liftover-1.5.0-cp315-cp315-win_amd64.whl
| Download URL | liftover-1.5.0-cp315-cp315-win_amd64.whl |
|---|---|
| Size | 381.4 kB |
| Tags | CPython 3.15 Windows x86-64 |
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Release files / liftover-1.5.0-cp315-cp315-musllinux_1_2_x86_64.whl
| Download URL | liftover-1.5.0-cp315-cp315-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.15 Linux musl 1.2+ x86-64 |
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Release files / liftover-1.5.0-cp315-cp315-musllinux_1_2_aarch64.whl
| Download URL | liftover-1.5.0-cp315-cp315-musllinux_1_2_aarch64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.15 Linux musl 1.2+ ARM64 |
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Release files / liftover-1.5.0-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
| Download URL | liftover-1.5.0-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl |
|---|---|
| Size | 888.0 kB |
| Tags | CPython 3.15 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64 |
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Release files / liftover-1.5.0-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
| Download URL | liftover-1.5.0-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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| Size | 948.8 kB |
| Tags | CPython 3.15 Linux glibc 2.17+ x86-64 |
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Release files / liftover-1.5.0-cp315-cp315-macosx_11_0_arm64.whl
| Download URL | liftover-1.5.0-cp315-cp315-macosx_11_0_arm64.whl |
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| Size | 161.3 kB |
| Tags | CPython 3.15 macOS 11.0+ ARM64 |
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Release files / liftover-1.5.0-cp314-cp314-win_amd64.whl
| Download URL | liftover-1.5.0-cp314-cp314-win_amd64.whl |
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| Size | 381.4 kB |
| Tags | CPython 3.14 Windows x86-64 |
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Release files / liftover-1.5.0-cp314-cp314-musllinux_1_2_x86_64.whl
| Download URL | liftover-1.5.0-cp314-cp314-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.14 Linux musl 1.2+ x86-64 |
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| Download URL | liftover-1.5.0-cp314-cp314-musllinux_1_2_aarch64.whl |
|---|---|
| Size | 1.8 MB |
| Tags | CPython 3.14 Linux musl 1.2+ ARM64 |
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| Download URL | liftover-1.5.0-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl |
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| Size | 888.4 kB |
| Tags | CPython 3.14 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64 |
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| Download URL | liftover-1.5.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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| Size | 946.5 kB |
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| Download URL | liftover-1.5.0-cp314-cp314-macosx_11_0_arm64.whl |
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| Size | 161.4 kB |
| Tags | CPython 3.14 macOS 11.0+ ARM64 |
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Release files / liftover-1.5.0-cp313-cp313-win_amd64.whl
| Download URL | liftover-1.5.0-cp313-cp313-win_amd64.whl |
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| Size | 373.0 kB |
| Tags | CPython 3.13 Windows x86-64 |
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| Download URL | liftover-1.5.0-cp313-cp313-musllinux_1_2_x86_64.whl |
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| Size | 1.9 MB |
| Tags | CPython 3.13 Linux musl 1.2+ x86-64 |
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| Download URL | liftover-1.5.0-cp313-cp313-musllinux_1_2_aarch64.whl |
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| Size | 1.8 MB |
| Tags | CPython 3.13 Linux musl 1.2+ ARM64 |
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| Download URL | liftover-1.5.0-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl |
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| Size | 888.4 kB |
| Tags | CPython 3.13 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64 |
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| Download URL | liftover-1.5.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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| Size | 948.7 kB |
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| Download URL | liftover-1.5.0-cp313-cp313-macosx_11_0_arm64.whl |
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| Download URL | liftover-1.5.0-cp312-cp312-win_amd64.whl |
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| Download URL | liftover-1.5.0-cp312-cp312-musllinux_1_2_x86_64.whl |
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| Size | 1.9 MB |
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| Download URL | liftover-1.5.0-cp312-cp312-musllinux_1_2_aarch64.whl |
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| Download URL | liftover-1.5.0-cp312-cp312-macosx_11_0_arm64.whl |
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| Download URL | liftover-1.5.0-cp311-cp311-win_amd64.whl |
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Release files / liftover-1.5.0-cp311-cp311-macosx_11_0_arm64.whl
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Release files / liftover-1.5.0-cp310-cp310-win_amd64.whl
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Release files / liftover-1.5.0-cp310-cp310-musllinux_1_2_x86_64.whl
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Release files / liftover-1.5.0-cp310-cp310-musllinux_1_2_aarch64.whl
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Release files / liftover-1.5.0-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / liftover-1.5.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
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Release files / liftover-1.5.0-cp310-cp310-macosx_11_0_arm64.whl
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Release files / liftover-1.5.0-cp39-cp39-win_amd64.whl
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Release files / liftover-1.5.0-cp39-cp39-musllinux_1_2_x86_64.whl
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Release files / liftover-1.5.0-cp39-cp39-musllinux_1_2_aarch64.whl
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Release files / liftover-1.5.0-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / liftover-1.5.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
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Release files / liftover-1.5.0-cp39-cp39-macosx_11_0_arm64.whl
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