Another Genome Conversion Tool: Python frontend to Rust chainfile crate

These details have not been verified by PyPI

Project links

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/).

Status: alpha.

Usage

Initialize a class instance:

from agct import Converter
c = Converter("hg38", "hg19")

Call convert_coordinate():

c.convert_coordinate("chr7", 140453136, "+")
# [['chr7', '140152936', '+']]

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]'

Be sure to install pre-commit hooks:

pre-commit install

This installs Python code as editable, but after any changes to Rust code, maturin develop must be run:

maturin develop

Run tests with pytest:

pytest

Project details

These details have not been verified by PyPI

Project links

Release history Release notifications | RSS feed

0.1.0.dev2 pre-release

Jun 4, 2024

0.1.0.dev1 pre-release

Feb 2, 2024

This version

0.1.0.dev0 pre-release

Jan 30, 2024

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

agct-0.1.0.dev0.tar.gz (9.0 kB view hashes)

Uploaded Jan 30, 2024 Source

Built Distributions

agct-0.1.0.dev0-cp38-abi3-win_amd64.whl (162.8 kB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ Windows x86-64

agct-0.1.0.dev0-cp38-abi3-win32.whl (158.3 kB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ Windows x86

agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ manylinux: glibc 2.17+ x86-64

agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.3 MB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ manylinux: glibc 2.17+ s390x

agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.2 MB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ manylinux: glibc 2.17+ ppc64le

agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.1 MB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ manylinux: glibc 2.17+ ARMv7l

agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.1 MB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ manylinux: glibc 2.17+ ARM64

agct-0.1.0.dev0-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.whl (1.2 MB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ manylinux: glibc 2.5+ i686

agct-0.1.0.dev0-cp38-abi3-macosx_11_0_arm64.whl (297.9 kB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ macOS 11.0+ ARM64

agct-0.1.0.dev0-cp38-abi3-macosx_10_12_x86_64.whl (297.8 kB view hashes)

Uploaded Jan 30, 2024 CPython 3.8+ macOS 10.12+ x86-64

Hashes for agct-0.1.0.dev0.tar.gz

Hashes for agct-0.1.0.dev0.tar.gz
Algorithm	Hash digest
SHA256	`aba51a9059cc5008217ecbca862b29b1290ec2fe0e9b07972174b737da72c9fd`
MD5	`8389638be8fd953145c283e7e2f19807`
BLAKE2b-256	`e2352eeb176d324e3708a90a63969c0bd36d08c94370d00df8b2ab8bda6d3349`

Hashes for agct-0.1.0.dev0-cp38-abi3-win_amd64.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-win_amd64.whl
Algorithm	Hash digest
SHA256	`33c710fcc50fbc72e708bf92543f216feaf4c09a30344be04e59be32918607e4`
MD5	`7832336d0e052f1cf9ccfe06b43b378d`
BLAKE2b-256	`f776234bf4f9f6bed7491ee80f89b8a85ab71ea0b7b0a71464ab7f56eacfb6d2`

Hashes for agct-0.1.0.dev0-cp38-abi3-win32.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-win32.whl
Algorithm	Hash digest
SHA256	`fcb1d9934fe6c05f464051ff7c77875f2ac73ee7b1d1a3728a3f0a613df5d4ed`
MD5	`4695a0d0964895033272ac62277ea929`
BLAKE2b-256	`40608bedaa20572331d424a6a1a516d975f852c8857e14f6ae32ca5e2f1bd97c`

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`b9ef375924ac86d350e93fed47509dbec89ba1489dcde30011475fdf35652352`
MD5	`939623fb2df1fa829663ca6d2f5ba3e2`
BLAKE2b-256	`3c5b1629bc912cb1e8e9d7e59066ad4aab8feb3c6ba1bb54ec092bce4bf89f40`

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl
Algorithm	Hash digest
SHA256	`09550d8d68044eb3cc3fba94cc227e502c1805b67a740b54f3bb01b873c16081`
MD5	`240dcee59c9b6e0215b0abfd44db73c5`
BLAKE2b-256	`ae6580dcb92cc1684b3ff32ddccea821369391a5296c0c550caa118a0137ff30`

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
Algorithm	Hash digest
SHA256	`47c8e08656bcf7c436be6dad1b55e375e482e7a99cbc90f168b5154c365438c1`
MD5	`87f41cfbd9e323342cd16e0570b1805d`
BLAKE2b-256	`7590e0a69e58007784904616fa90a569dd6d2ed968ea47d8391d6d0b5604fc03`

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
Algorithm	Hash digest
SHA256	`b3a0ce4c6751a7b91daa07cd3842959fdac046cd7a759b1a2291014885c93377`
MD5	`46eae9b5306d7b560b1be569376f0bf9`
BLAKE2b-256	`e38475786e297e9125134a2424a8694f13a2abcbd664b856a78a64380dd35c98`

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Algorithm	Hash digest
SHA256	`74d2ec229e5e10698cd8184f00b7abc237a510e75a790a0bd786669ec2f6d536`
MD5	`cae606308c9ef3a7e9b9f3a21f46e74a`
BLAKE2b-256	`b61999bc01867e0363005cb333ff6ef4b9a61899b5881809b9451faca26a1478`

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.whl
Algorithm	Hash digest
SHA256	`541aeac0137a9e89802b096ab53111ed313f7b16c77f717071f1c24d790121fe`
MD5	`506901d571ba0d2a3206d31092aa93db`
BLAKE2b-256	`cd0b5cc3a725bcca0d5e695d548ae48eab8303390f2b6be2aaf2e98b6f532f96`

Hashes for agct-0.1.0.dev0-cp38-abi3-macosx_11_0_arm64.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-macosx_11_0_arm64.whl
Algorithm	Hash digest
SHA256	`112ac5ee7c6019b2eec9e045a257eea455ae7dd49f94eb0f83b0c30fc69beb36`
MD5	`07e01ca81cde493ef4dfcec0a4da12f1`
BLAKE2b-256	`efd9bf0984248847485bed933fc62bd585b3999defce8f6d2d9ccaf29bce9c74`

Hashes for agct-0.1.0.dev0-cp38-abi3-macosx_10_12_x86_64.whl

Hashes for agct-0.1.0.dev0-cp38-abi3-macosx_10_12_x86_64.whl
Algorithm	Hash digest
SHA256	`df4701f84a5146fc843689551d14f8cef3f47770af9c4b4a5ddb6333676c3000`
MD5	`06cb6dcad6ac7114eb4ba0afe00df08f`
BLAKE2b-256	`31193b4ecc38b1510ca95fdf5fc89325c6a33412cfb8c01903a8b716c4297f22`