dark-matter

(Pure) Python scripts and libraries for bioinformatics.

Source code: github.com/acorg/dark-matter

Overview

Utility scripts

The bin directory contains over 100 utility scripts. See Scripts for the full list, grouped into categories such as:

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

The dark library, under src/dark, is documented in Library for developers who want to write their own code against it, grouped into categories such as:

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

See Reads for a dedicated explanation of the central Read class hierarchy that underlies most of the above.

Installation

pip install dark-matter

or, using uv:

uv add dark-matter

dark-matter supports Python 3.10 through 3.15.

License

MIT. See LICENSE.