{"id":16916943,"url":"https://github.com/althonos/rich-msa","last_synced_at":"2025-09-12T16:33:16.493Z","repository":{"id":39493398,"uuid":"490747111","full_name":"althonos/rich-msa","owner":"althonos","description":"A Rich renderable for viewing Multiple Sequence Alignments in the 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`rich-msa` [![Stars](https://img.shields.io/github/stars/althonos/rich-msa.svg?style=social\u0026maxAge=3600\u0026label=Star)](https://github.com/althonos/rich-msa/stargazers)\n\n*A simple module to render colorful Multiple Sequence Alignment with `rich` in the terminal.*\n\n[![Actions](https://img.shields.io/github/workflow/status/althonos/rich-msa/Test/main?logo=github\u0026style=flat-square\u0026maxAge=300)](https://github.com/althonos/rich-msa/actions)\n[![Coverage](https://img.shields.io/codecov/c/gh/althonos/rich-msa?style=flat-square\u0026maxAge=3600)](https://codecov.io/gh/althonos/rich-msa/)\n[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square\u0026maxAge=2678400)](https://choosealicense.com/licenses/mit/)\n[![PyPI](https://img.shields.io/pypi/v/rich-msa.svg?style=flat-square\u0026maxAge=3600)](https://pypi.org/project/rich-msa)\n[![Wheel](https://img.shields.io/pypi/wheel/rich-msa.svg?style=flat-square\u0026maxAge=3600)](https://pypi.org/project/rich-msa/#files)\n[![Python Versions](https://img.shields.io/pypi/pyversions/rich-msa.svg?style=flat-square\u0026maxAge=3600)](https://pypi.org/project/rich-msa/#files)\n[![Python Implementations](https://img.shields.io/badge/impl-universal-success.svg?style=flat-square\u0026maxAge=3600\u0026label=impl)](https://pypi.org/project/rich-msa/#files)\n[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400\u0026style=flat-square)](https://github.com/althonos/rich-msa/)\n[![Mirror](https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square\u0026maxAge=2678400)](https://git.embl.de/larralde/rich-msa/)\n[![GitHub issues](https://img.shields.io/github/issues/althonos/rich-msa.svg?style=flat-square\u0026maxAge=600)](https://github.com/althonos/rich-msa/issues)\n[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400\u0026style=flat-square)](https://github.com/althonos/rich-msa/blob/master/CHANGELOG.md)\n[![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square\u0026color=303f9f\u0026maxAge=86400\u0026label=downloads\u0026query=%24.total_downloads\u0026url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Frich-msa)](https://pepy.tech/project/rich-msa)\n\n\n## 🔧 Installing\n\nInstall the `rich-msa` package directly from [PyPi](https://pypi.org/project/rich-msa)\nwhich hosts universal wheels that can be installed with `pip`:\n```console\n$ pip install rich-msa\n```\n\n## 💡 Example\n\nUse Biopython to load a MSA from an aligned FASTA file, and render it to the\nterminal:\n\n```python\nimport Bio.AlignIO\nimport rich\nfrom rich_msa import RichAlignment\n\nmsa = Bio.AlignIO.read(\"tests/data/swissprot-halorhodopsin.muscle.afa\", \"fasta\")\nviewer = RichAlignment(\n    names=[record.id for record in msa],\n    sequences=[str(record.seq) for record in msa],\n)\n\npanel = rich.panel.Panel(viewer, title=\"swissprot-halorhodopsin.muscle.afa\")\nrich.print(panel)\n```\n\nYou should get an output similar to the following picture, scaled to your\nterminal width:\n![screenshot](https://github.com/althonos/rich-msa/raw/main/static/example1.png)\n\n\n## 🪛 Command-Line\n\nIf you have the `rich-msa` library installed from PyPI, you can use it directly\nto view any alignment file, provided you have [Biopython](https://biopython.org) installed:\n\n```console\n$ python -m rich_msa -i tests/data/swissprot-halorhodopsin.muscle.afa\n```\n\n*Use the `-f` flag to change the file format from aligned FASTA (default) to\nany alignment format supported by Biopython.*\n\n## 💭 Feedback\n\n### ⚠️ Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue\ntracker](https://github.com/althonos/rich-msa/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n### 🏗️ Contributing\n\nContributions are more than welcome! See\n[`CONTRIBUTING.md`](https://github.com/althonos/rich-msa/blob/main/CONTRIBUTING.md)\nfor more details.\n\n## ⚖️ License\n\nThis library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the [original Rich authors](https://github.com/textualize). It was developed\nby [Martin Larralde](https://github.com/althonos/) during his PhD project\nat the [European Molecular Biology Laboratory](https://www.embl.de/) in\nthe [Zeller team](https://github.com/zellerlab).*\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falthonos%2Frich-msa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falthonos%2Frich-msa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falthonos%2Frich-msa/lists"}