@deckyard/bioinformatics

Sequence manipulation for DNA, RNA and protein in Jennifer, modelled on the Sequence Manipulation Suite: transforms, composition and physical properties, pattern, ORF and restriction-site search, FASTA and FASTQ, random sequences, and pairwise alignment. Sequences are plain strings. Nothing under src/ touches the network, a subprocess or the filesystem, so the deck needs no capability and runs on jennifer-tiny.

Documentation

Install

jvc add @deckyard/bioinformatics

This vendors the deck to vendor/deckyard/bioinformatics/. Without jvc, unpack the src/ subtree of a release archive (deckyard-bioinformatics-<version>.tar.gz) there. Requires Jennifer 0.26.0 or newer; no deck dependencies.

Usage

import "@deckyard/bioinformatics/" as bioseq;

def gene as string init bioseq.filterDna("1 atg acg tta cat gga taa");

bioseq.reverseComplement($gene);            # TTATCCATGTAACGTCAT
bioseq.translate($gene);                    # MTLHG*
bioseq.gcContent($gene);                    # 33.33
bioseq.molecularWeight($gene, bioseq.DNA);  # 5546.66

Development

tools/check-all.sh                          # the full gate, as CI runs it
jennifer test src/bioinformatics_test.j     # the test suite
jennifer run examples/transforms.j          # one example per topic in examples/
jennifer lint src/bioinformatics.j src/bioinformatics_test.j

A topic file cannot be linted alone: it is included, so lint the entry module and the test overlay, which splice every topic. src/topics/tabledata.j and src/topics/enzymedata.j are generated; see tools/README.md.

The book's source is docs/, built with Grimoire. To read it locally:

git clone https://github.com/jennifer-language/grimoire .grimoire
jennifer run .grimoire/bin/grimoire serve

Licence

LGPL-3.0-only, see LICENSE. Copyright (C) 2026 mplx <[email protected]>.