Proksee Batch is a command-line tool for visualizing multiple prokaryotic genomes via the Proksee web application. Instead of manually uploading each genome to Proksee and manually configuring the visualization, Proksee Batch allows you to, with a single command, upload multiple genomes with custom configuration options, add features from additonal files, and obtain links to Proksee projects for further analysis of each genome. Also, Proksee Batch is designed to be included in bioinformatics workflows/pipelines for analyzing hundreds of genomes efficiently and reproducibly.
The main advantage over alternative command-line genome visualization tools is that Proksee Batch provides access to the genome information in the form of an interactive Proksee map that supports zooming to the nucleotide level and that is linked to numerous additional tools for further genome analysis via the graphical interface. The genome maps can also be easily customized within Proksee and exported in a variety of formats.
You can simply install Proksee Batch via pip from PyPI:
pip install proksee-batchOr, better yet, use pipx to install Proksee Batch from PyPI in an isolated environment:
pipx install proksee-batchTo install Proksee Batch in a conda environment, use a YAML file like this:
name: proksee-batch
channels:
- conda-forge
dependencies:
- python=3.11
- pip
- pip:
- proksee-batchPlease see the Command-line Reference for details.
Contributions are welcome. To learn more, see the Contributor Guide.
Distributed under the terms of the MIT license, Proksee Batch is free and open source software.
If you encounter any problems, please file an issue along with a detailed description.
Authors: Lael Barlow and Jason Grant
This project was initially generated using @cjolowicz's Hypermodern Python Cookiecutter template.