scATAC Fragment Tools

Tools for manipulating scATAC-seq fragment files.

Installation

From PyPI

# 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

# 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