{"name":"@deckyard/bioinformatics","description":"sequence manipulation for DNA, RNA and protein","versions":{"0.2.0":{"version":"0.2.0","kind":"git","url":"https://github.com/deckyard/deck-bioinformatics.git","ref":"0.2.0","commit":"2b12e22831722a5a6362a275138bd181796ca2df","checksum":"","yanked":false,"license":"LGPL-3.0-only","requires":{},"engines":{"jennifer":"\u003e=0.25.0","jennifer-tiny":"\u003e=0.25.0"},"capabilities":[],"keywords":["bioinformatics","dna","rna","protein","sequence"],"description":"sequence manipulation for DNA, RNA and protein","publishedAt":"1793615611","repoId":1350404933,"repoOwnerId":346943577,"repoOwner":"deckyard"},"0.3.0":{"version":"0.3.0","kind":"git","url":"https://github.com/deckyard/deck-bioinformatics.git","ref":"0.3.0","commit":"71f87dd63ad8896d957a88d12ea8f807f9cd7e54","checksum":"","yanked":false,"license":"LGPL-3.0-only","requires":{},"engines":{"jennifer":"\u003e=0.26.0","jennifer-tiny":"\u003e=0.26.0"},"capabilities":[],"keywords":["bioinformatics","dna","rna","protein","sequence"],"description":"sequence manipulation for DNA, RNA and protein","publishedAt":"1793916317","repoId":1350404933,"repoOwnerId":346943577,"repoOwner":"deckyard"}},"readme":"# @deckyard/bioinformatics\n\n[![test](https://github.com/deckyard/deck-bioinformatics/actions/workflows/test.yml/badge.svg)](https://github.com/deckyard/deck-bioinformatics/actions/workflows/test.yml)\n[![Documentation](https://img.shields.io/badge/docs-github%20pages-blue)](https://deckyard.github.io/deck-bioinformatics/)\n[![release](https://img.shields.io/github/v/release/deckyard/deck-bioinformatics)](https://github.com/deckyard/deck-bioinformatics/releases/latest)\n\nSequence manipulation for DNA, RNA and protein in\n[Jennifer](https://jennifer-lang.dev/), modelled on the Sequence Manipulation\nSuite: transforms, composition and physical properties, pattern, ORF and\nrestriction-site search, FASTA and FASTQ, random sequences, and pairwise\nalignment. Sequences are plain strings. Nothing under `src/` touches the\nnetwork, a subprocess or the filesystem, so the deck needs no capability and\nruns on `jennifer-tiny`.\n\n**[Documentation](https://deckyard.github.io/deck-bioinformatics/)**\n\n## Install\n\n```sh\njvc add @deckyard/bioinformatics\n```\n\nThis vendors the deck to `vendor/deckyard/bioinformatics/`. Without `jvc`, unpack\nthe `src/` subtree of a release archive\n(`deckyard-bioinformatics-\u003cversion\u003e.tar.gz`) there. Requires Jennifer 0.26.0 or\nnewer; no deck dependencies.\n\n## Usage\n\n```jennifer\nimport \"@deckyard/bioinformatics/\" as bioseq;\n\ndef gene as string init bioseq.filterDna(\"1 atg acg tta cat gga taa\");\n\nbioseq.reverseComplement($gene);            # TTATCCATGTAACGTCAT\nbioseq.translate($gene);                    # MTLHG*\nbioseq.gcContent($gene);                    # 33.33\nbioseq.molecularWeight($gene, bioseq.DNA);  # 5546.66\n```\n\n## Development\n\n```sh\ntools/check-all.sh                          # the full gate, as CI runs it\njennifer test src/bioinformatics_test.j     # the test suite\njennifer run examples/transforms.j          # one example per topic in examples/\njennifer lint src/bioinformatics.j src/bioinformatics_test.j\n```\n\nA topic file cannot be linted alone: it is `include`d, so lint the entry module\nand the test overlay, which splice every topic. `src/topics/tabledata.j` and\n`src/topics/enzymedata.j` are generated; see [`tools/README.md`](tools/README.md).\n\nThe book's source is [`docs/`](docs/), built with\n[Grimoire](https://github.com/jennifer-language/grimoire). To read it locally:\n\n```sh\ngit clone https://github.com/jennifer-language/grimoire .grimoire\njennifer run .grimoire/bin/grimoire serve\n```\n\n## Licence\n\nLGPL-3.0-only, see [LICENSE](LICENSE). Copyright (C) 2026 mplx \u0026lt;mplx@jennifer-lang.dev\u0026gt;.\n"}