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:
- FASTA/FASTQ: general sequence inspection, filtering, and manipulation
- DNA/amino-acid translation and codon tools
- Pairwise sequence comparison
- Multiple-sequence-alignment (MSA) and alignment-position analysis
- Consensus-sequence building
- Read mapping and SAM/BAM analysis
- BLAST/DIAMOND hit processing and alignment panels
- Protein/genome SQLite databases and GenBank data
- Taxonomy
- Phylogenetic trees (Newick)
Library functions
- Core reads & sequence I/O
- DNA & amino-acid biology
- Sequence alignment & comparison
- Alignment-result containers, filtering & summarization
- BLAST
- DIAMOND
- SAM/BAM, read mapping & consensus building
- Protein/genome databases, GenBank & taxonomy
- Phylogenetic trees
- Visualization: plotting & HTML
- General utilities
Installation
pip install dark-matter
or, using uv:
uv add dark-matter
dark-matter supports Python 3.10 through 3.15.
Documentation
doc/scripts.md— the command-line scripts inbin, for people who just want to run existing tools.doc/library.md— thedarkPython library undersrc/dark, for developers who want to write their own code against it.
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.
5 maintainers
Metadata
5 maintainers
Release files for dark-matter 7.5.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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Release files / dark_matter-7.5.0.tar.gz
| Download URL | dark_matter-7.5.0.tar.gz |
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| Size | 502.3 kB |
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