Metadata-Version: 2.4
Name: scatac_fragment_tools
Version: 0.1.5
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Dist: numpy
Requires-Dist: polars>=1.32.0
Requires-Dist: pyarrow
Requires-Dist: numba
Requires-Dist: rich-argparse
Requires-Dist: joblib
Requires-Dist: mypy ; extra == 'development'
Requires-Dist: ruff ; extra == 'development'
Requires-Dist: pytest ; extra == 'development'
Requires-Dist: pybigtools>=0.2.4 ; extra == 'pybigtools'
Requires-Dist: pybigwig ; extra == 'pybigwig'
Provides-Extra: development
Provides-Extra: pybigtools
Provides-Extra: pybigwig
License-File: LICENSE
Summary: Tools for working with scATAC-seq fragment files.
Keywords: scATAC-seq,scATAC,fragment files
Requires-Python: >=3.10
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: changelog, https://raw.githubusercontent.com/aertslab/scatac_fragment_tools/CHANGELOG.md
Project-URL: documentation, https://aertslab.github.io/scatac_fragment_tools/
Project-URL: homepage, https://github.com/aertslab/scatac_fragment_tools/
Project-URL: repository, https://github.com/aertslab/scatac_fragment_tools/

# scATAC Fragment Tools

[![PyPI](https://img.shields.io/pypi/v/scatac-fragment-tools?color=green)](https://pypi.org/project/scatac-fragment-tools/)
[![Docs](https://img.shields.io/badge/Docs-blue)](https://aertslab.github.io/scatac_fragment_tools/)

Tools for manipulating scATAC-seq fragment files.


## Installation

### From PyPI

```bash
# Install scatac-fragment-tools.
pip install scatac-fragment-tools

# To use "scatac_fragment_tools bigwig", you need to install "pybigtools" (fastest) or "pybigwig".
pip install scatac-fragment-tools[pybigtools]
pip install scatac-fragment-tools[pybigwig]
```

### From source

```bash
# Install maturin.
pip install maturin

# Or install maturin with zig support (to build wheel that can run on older Linux distributions).
pip install maturin[zig]

# Clone scatac_fragments_tools git repo.
git clone https://github.com/aertslab/scatac_fragment_tools.git

cd scatac_fragment_tools

# Install in developer mode (aka `pip install -e .`)
maturin develop --release

# Or build a wheel and install afterwards with pip.
maturin build --release
# pip install rust/target/wheels/scatac_fragment_tools-${scatac_tools_version}-cp${python_version}-abi3-manylinux_${glibc_version}_x86_64.whl

# Or build a wheel that is more distributable (would still run on CentOS7).
maturin build --release --compatibility manylinux2014 --zig
# pip install rust/target/wheels/scatac_fragment_tools-${scatac_tools_version}-cp${python_version}-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
```


## Usage

Please visit the [documentation](https://aertslab.github.io/scatac_fragment_tools/)

