Dark matter

(Pure) Python scripts and libraries for bioinformatics.

Overview

Utility scripts

The bin directory contains over 100 utility scripts. These fall into the following categories:

1. FASTA/FASTQ: general sequence inspection, filtering, and manipulation
2. DNA/amino-acid translation and codon tools
3. Pairwise sequence comparison
4. Multiple-sequence-alignment (MSA) and alignment-position analysis
5. Consensus-sequence building
6. Read mapping and SAM/BAM analysis
7. BLAST/DIAMOND hit processing and alignment panels
8. Protein/genome SQLite databases and GenBank data
9. Taxonomy
10. Phylogenetic trees (Newick)

Library functions

1. Core reads & sequence I/O
2. DNA & amino-acid biology
3. Sequence alignment & comparison
4. Alignment-result containers, filtering & summarization
5. BLAST
6. DIAMOND
7. SAM/BAM, read mapping & consensus building
8. Protein/genome databases, GenBank & taxonomy
9. Phylogenetic trees
10. Visualization: plotting & HTML
11. General utilities

Installation

pip install dark-matter

or, using uv:

uv add dark-matter

dark-matter supports Python 3.10 through 3.15.

Documentation

The full documentation is at acorg.github.io/dark-matter, built from the Markdown files below:

• doc/scripts.md — the command-line scripts in bin, for people who just want to run existing tools.
• doc/library.md — the dark Python library under src/dark, for developers who want to write their own code against it.
• doc/reads.md — the central Read class hierarchy.

Developers

git clone https://github.com/acorg/dark-matter.git
cd dark-matter
uv sync

Run the tests with

make pytest

or directly via

uv run pytest

License

MIT. See LICENSE.