Installation

Requirements

Requirement	Version	Needed for
Python	≥ 3.12	everything
samtools	any recent	indexing FASTA/BAM; used by `index` and `align`
bwa	any recent	`index` and `align` only

samtools and bwa must be on your PATH for the index and align commands. The signal/QC commands (bam2bw, bam2fragment, qc) do not require them.

# macOS (Homebrew)
brew install samtools bwa

# Ubuntu / Debian
sudo apt-get install samtools bwa

# conda
conda install -c bioconda samtools bwa

Install DeamTools

From PyPI (recommended)

pip install deamtools
# or
uv pip install deamtools

To also install the optional seq2edit model, which pulls in PyTorch:

pip install "deamtools[seq2edit]"

From GitHub

pip install git+https://github.com/lzj1769/deamTools.git

Development install

The project is managed with uv, and uv.lock is committed, so uv sync reproduces the development environment exactly:

git clone https://github.com/lzj1769/deamTools.git
cd deamTools
uv sync --extra dev
uv run pytest

This additionally installs pytest, pytest-cov, ruff, black, and mypy. Run tools through uv run (for example uv run ruff check src/ tests/); there is no need to activate the environment.

Documentation extras

This documentation is built with Sphinx (MyST Markdown + the Read the Docs theme). To build it locally:

uv sync --extra docs
uv run sphinx-build -b html docs docs/_build/html
# open docs/_build/html/index.html

Python dependencies

Installed automatically by pip:

Package	Purpose
`numpy`	Per-base count arrays and signal convolution
`pandas`	Tabular / BED data utilities
`matplotlib`	Plotting (QC report, motif logo)
`logomaker`	Deaminase motif logo in the `qc` report
`pysam`	BAM and FASTA I/O
`pyBigWig`	BigWig reading and writing
`motifmatchpy`	Motif scanning (`match`)

The match command additionally needs the optional pyjaspar package to fetch motifs from JASPAR: pip install pyjaspar.

Verify installation

deamtools --version
# deamtools 0.1.4

deamtools --help

Running tests

cd deamTools
uv run pytest

The test suite uses synthetic BAM and FASTA fixtures created in a temporary directory, so no external data files — and no bwa/samtools — are required to run it.