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Description:

richmsa 0.1.0

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.