agct: Another Genome Conversion Tool
Lift over positions between genomic reference assemblies, using the St. Jude's chainfile crate.
Enables significantly faster chainfile loading from cold start (see analysis/).
Installation
Install from PyPI:
python3 -m pip install agct
Usage
Initialize a class instance:
from agct import Converter, Assembly, Strand
c = Converter(Assembly.HG19, Assembly.HG38)
If a chainfile is unavailable locally, it's downloaded from UCSC and saved using the
wags-tailspackage -- see the wags-tails configuration instructions for information on how to designate a non-default storage location.
Call convert_coordinate():
c.convert_coordinate("chr7", 140453136, 140453137, Strand.POSITIVE)
# returns [LiftoverResult(chrom='chr7', start=140753336, end=140753337, strand=<Strand.POSITIVE: '+'>, score=14633688187)]
Development
The Rust toolchain must be installed.
Create a virtual environment and install developer dependencies:
python3 -m virtualenv venv
source venv/bin/activate
python3 -m pip install -e '.[dev,tests]'
This installs Python code as editable, but after any changes to Rust code, run maturin develop to rebuild the Rust binary:
maturin develop
Be sure to install pre-commit hooks:
pre-commit install
Check Python style with ruff:
python3 -m ruff format . && python3 -m ruff check --fix .
Use cargo fmt to check Rust style (must be run from within the rust/ subdirectory):
cd rust/
cargo fmt
Run tests with pytest:
pytest
3 maintainers
Release files for agct 0.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| agct-0.2.1.tar.gz | 14.3 kB | Details |
Built distributions (wheels)
Total release size: 6.5 MB
Release files / agct-0.2.1.tar.gz
| Download URL | agct-0.2.1.tar.gz |
|---|---|
| Size | 14.3 kB |
| Tags | Source |
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maturin/1.12.6
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Release files / agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl |
|---|---|
| Size | 378.6 kB |
| Tags | Linux glibc 2.17+ IBM System/390x PyPy 3.10 PyPy 3.10 7.3 |
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Yes |
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maturin/1.12.6
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Release files / agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
| Download URL | agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
|---|---|
| Size | 476.5 kB |
| Tags | Linux glibc 2.17+ PowerPC 64-le PyPy 3.10 PyPy 3.10 7.3 |
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| Uploaded via |
maturin/1.12.6
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Release files / agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 357.7 kB |
| Tags | Linux glibc 2.17+ ARMv7l PyPy 3.10 PyPy 3.10 7.3 |
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| Uploaded via |
maturin/1.12.6
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Release files / agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | agct-0.2.1-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 347.2 kB |
| Tags | Linux glibc 2.17+ ARM64 PyPy 3.10 PyPy 3.10 7.3 |
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Release files / agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl |
|---|---|
| Size | 379.2 kB |
| Tags | Linux glibc 2.17+ IBM System/390x PyPy 3.9 PyPy 3.9 7.3 |
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Release files / agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
| Download URL | agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
|---|---|
| Size | 476.9 kB |
| Tags | Linux glibc 2.17+ PowerPC 64-le PyPy 3.9 PyPy 3.9 7.3 |
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Release files / agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 358.4 kB |
| Tags | Linux glibc 2.17+ ARMv7l PyPy 3.9 PyPy 3.9 7.3 |
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Release files / agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | agct-0.2.1-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 348.2 kB |
| Tags | Linux glibc 2.17+ ARM64 PyPy 3.9 PyPy 3.9 7.3 |
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Release files / agct-0.2.1-cp310-abi3-win_amd64.whl
| Download URL | agct-0.2.1-cp310-abi3-win_amd64.whl |
|---|---|
| Size | 205.0 kB |
| Tags | CPython 3.10 Windows x86-64 abi3 |
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| Download URL | agct-0.2.1-cp310-abi3-win32.whl |
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| Size | 198.0 kB |
| Tags | CPython 3.10 Windows x86-32 abi3 |
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Release files / agct-0.2.1-cp310-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | agct-0.2.1-cp310-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl |
|---|---|
| Size | 378.9 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ IBM System/390x abi3 |
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| Download URL | agct-0.2.1-cp310-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
|---|---|
| Size | 477.7 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ PowerPC 64-le abi3 |
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| Download URL | agct-0.2.1-cp310-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 358.7 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARMv7l abi3 |
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| Download URL | agct-0.2.1-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 347.8 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 abi3 |
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| Size | 312.9 kB |
| Tags | CPython 3.10 abi3 macOS 11.0+ ARM64 |
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| Size | 317.9 kB |
| Tags | CPython 3.10 abi3 macOS 10.12+ x86-64 |
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| Size | 354.6 kB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
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| Size | 382.2 kB |
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