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=3.13
- 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.
1 maintainer
Metadata
1 maintainer
Release files for proksee-batch 0.6.11
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| proksee_batch-0.6.11.tar.gz | 7.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| proksee_batch-0.6.11-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 15.8 MB
Release files / proksee_batch-0.6.11.tar.gz
| Download URL | proksee_batch-0.6.11.tar.gz |
|---|---|
| Size | 7.7 MB |
| Tags | Source |
|
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No |
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twine/5.0.0 CPython/3.12.11
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Release files / proksee_batch-0.6.11-py3-none-any.whl
| Download URL | proksee_batch-0.6.11-py3-none-any.whl |
|---|---|
| Size | 8.0 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.0.0 CPython/3.12.11
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