A Rich renderable for viewing Multiple Sequence Alignments in the terminal.

Martin Larralde

Last update: Dec 4, 2022

Related tags

Third-party APIs Wrappers rich-msa

Overview

`rich-msa`

A simple module to render colorful Multiple Sequence Alignment with rich in the terminal.

🔧 Installing

Install the rich-msa package directly from PyPi which hosts universal wheels that can be installed with pip:

$ pip install rich-msa

💡 Example

Use Biopython to load a MSA from an aligned FASTA file, and render it to the terminal:

import Bio.AlignIO
import rich
from rich_msa import RichAlignment

msa = Bio.AlignIO.read("tests/data/swissprot-halorhodopsin.muscle.afa", "fasta")
viewer = RichAlignment(
    names=[record.id for record in msa],
    sequences=[str(record.seq) for record in msa],
)

panel = rich.panel.Panel(viewer, title="swissprot-halorhodopsin.muscle.afa")
rich.print(panel)

You should get an output similar to the following picture, scaled to your terminal width:

🪛 Command-Line

If you have the rich-msa library installed from PyPI, you can use it directly to view any alignment file, provided you have Biopython installed:

$ python -m rich_msa -i tests/data/swissprot-halorhodopsin.muscle.afa

Use the -f flag to change the file format from aligned FASTA (default) to any alignment format supported by Biopython.

💭 Feedback

⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.

🏗️ Contributing

Contributions are more than welcome! See CONTRIBUTING.md for more details.

⚖️ License

This library is provided under the MIT License.

This project is in no way not affiliated, sponsored, or otherwise endorsed by the original Rich authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.

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Comments

Can this tools generate a PDF or svg file?

Hi, It is such an amazing tools! I love this pattern to show the msa results. But I am wondering if it can generante a PDF file that contain the output show in the terminal?

Lan
question

opened by Orz-CQ 1