Another Genome Conversion Tool: Python frontend to Rust chainfile crate
Project description
agct: Another Genome Conversion Tool
Drop-in replacement for the pyliftover tool, 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, Genome
c = Converter(Genome.HG38, Genome.HG19)
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, "+")
# [['chr7', 140152936, <Strand.POSITIVE: '+'>]]
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
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
File details
Details for the file agct-0.1.0.dev2.tar.gz.
File metadata
- Download URL: agct-0.1.0.dev2.tar.gz
- Upload date:
- Size: 10.6 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 09527a97d1427b64803bb268de32822ad21082c94a084a1d4a9880a6c956bf33 |
|
| MD5 | 05d2be8c4851f7e5674a44cd15df4a4c |
|
| BLAKE2b-256 | 851f2245f3e7c5938aa35fff59f5b08eb9d378cb645a12ed55156550eaa3dd41 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-win_amd64.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-win_amd64.whl
- Upload date:
- Size: 163.8 kB
- Tags: CPython 3.8+, Windows x86-64
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | d53eb39fca8f579d3ab962b9f3597013b127707d49101956f67ecb4054b85865 |
|
| MD5 | 73d57b637e4e78d9afed3ecbbe0b6784 |
|
| BLAKE2b-256 | 5f3aca47f10e7f6b8c09264cca7d113277eb4909eaf24db2ed4541421165eab7 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-win32.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-win32.whl
- Upload date:
- Size: 161.3 kB
- Tags: CPython 3.8+, Windows x86
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 0ce8e03b42c72051d8eda4113e6246ac1f9778cf67a3719263fae3f5bed23dbf |
|
| MD5 | f11367f7d3effbe69997f817e8601bf5 |
|
| BLAKE2b-256 | af7f6be759f845aee26e0b70aacbfc76fb9823da2c7dae5d0e9fcc30485c5751 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
- Upload date:
- Size: 1.1 MB
- Tags: CPython 3.8+, manylinux: glibc 2.17+ x86-64
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 40a87d4777c512cb02159fef069d048b04c208809d3fe0657ce244f498ef3956 |
|
| MD5 | 94071d7bc783341e7d7d3549a89703f5 |
|
| BLAKE2b-256 | cb1fd1d515e167e4145988623d36fdbea5e47c4e8a624f6a6eee5db6d3bb2f76 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl
- Upload date:
- Size: 1.2 MB
- Tags: CPython 3.8+, manylinux: glibc 2.17+ s390x
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 185022922fe52bc2418f9c2d473dd3ba8a0c86aef1229b5faf4c3e77b70c26a0 |
|
| MD5 | 1a3cb9f042887bd852f5679afcfa4225 |
|
| BLAKE2b-256 | b2fd4e7cee6ba9e4027ed8a1280011a06ef3fb92f3bdc932d60ede95f8d24d69 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
- Upload date:
- Size: 1.1 MB
- Tags: CPython 3.8+, manylinux: glibc 2.17+ ppc64le
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 39196487e1ea35cf9a891afd7eb102273b9ff0ca8cc81e4d2113135ac3a677f9 |
|
| MD5 | 2eb840a894ae6140c6dd2534d5bc9040 |
|
| BLAKE2b-256 | 2612c825dc5030d595ee816d6033312784d77102baa3c08794ef60ec41ed2458 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
- Upload date:
- Size: 1.1 MB
- Tags: CPython 3.8+, manylinux: glibc 2.17+ ARMv7l
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 96aa4474f484ffd446e5b15be9da773b289d8bae61e94ae576ea6dcff63fd109 |
|
| MD5 | 28028839975b2df11c9c05c299e173e6 |
|
| BLAKE2b-256 | 62f488839410270a64cefbf084a83b0de7af8c1178a0d2f1893e068913dc6392 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
- Upload date:
- Size: 1.1 MB
- Tags: CPython 3.8+, manylinux: glibc 2.17+ ARM64
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | cc1b4d8331480d105e540ae68629f5da84a22c7fe184cd2f52822830bbc78913 |
|
| MD5 | c43f818fc1fd299a78dbd070127f74b0 |
|
| BLAKE2b-256 | dc5fbd0031cbfe77408641da3a4097f1b21419d959544c678417f7ae6e309239 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.whl
- Upload date:
- Size: 1.1 MB
- Tags: CPython 3.8+, manylinux: glibc 2.5+ i686
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 6360f660bae1cb08293a62a525f10485e19fc351bd6f0242b7bd7ee409c99055 |
|
| MD5 | b409bb8d853d26a3c130144ed693673f |
|
| BLAKE2b-256 | 094527bda0a5e3c65daa0bf5d0173ad1c3bd83b802dd03005ace9daa99d3720d |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-macosx_11_0_arm64.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-macosx_11_0_arm64.whl
- Upload date:
- Size: 274.5 kB
- Tags: CPython 3.8+, macOS 11.0+ ARM64
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e3cb94bbca76d4987714118de15f8f604cff0349f023f929d04f61518f8125ce |
|
| MD5 | d4c0bb04d7edb35fac06a6a55ab3853f |
|
| BLAKE2b-256 | 11232426a67b86831937882f4f92ad145dcc784d5ce30128c039e08e961c1f79 |
File details
Details for the file agct-0.1.0.dev2-cp38-abi3-macosx_10_12_x86_64.whl.
File metadata
- Download URL: agct-0.1.0.dev2-cp38-abi3-macosx_10_12_x86_64.whl
- Upload date:
- Size: 277.8 kB
- Tags: CPython 3.8+, macOS 10.12+ x86-64
- Uploaded using Trusted Publishing? Yes
- Uploaded via: maturin/1.6.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 68cabfc377928ead9c2b2943e299af9d00bd153a3eeb9dad9dbaccaf2aab6c98 |
|
| MD5 | 719320d634f9ea68772c88a406530f0f |
|
| BLAKE2b-256 | 77b512d76acee77931c9cb2c795f261d40c52491d07445c98d84dd66b007bf03 |
