proksee-batch 0.5.1

Proksee Batch

Proksee Batch

Features

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.

Installation

You can simply install Proksee Batch via pip from PyPI:

pip install proksee-batch

Or, better yet, use pipx to install Proksee Batch from PyPI in an isolated environment:

pipx install proksee-batch

To 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-batch

Usage

Please see the Command-line Reference for details.

Contributing

Contributions are welcome. To learn more, see the Contributor Guide.

License

Distributed under the terms of the MIT license, Proksee Batch is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Credits

Authors: Lael Barlow and Jason Grant

This project was initially generated using @cjolowicz's Hypermodern Python Cookiecutter template.