Metadata-Version: 2.4
Name: proGenomes
Version: 0.2.0
Summary: A proGenomes command-line tool for interacting with bacterial and archeal genomes.
Author-email: proGenomes Development Team <luispedro@big-data-biology.org>
Maintainer-email: Alexandre Areias Castro <alexandre@big-data-biology.org>
License-Expression: MIT
Project-URL: Homepage, https://github.com/BigDataBiology/progenomes
Project-URL: Bug Reports, https://github.com/BigDataBiology/progenomes/issues
Project-URL: Source, https://github.com/BigDataBiology/progenomes
Keywords: bioinformatics,microbiology,metagenomics
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Software Development :: Build Tools
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Healthcare Industry
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Operating System :: OS Independent
Classifier: Natural Language :: English
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: polars
Requires-Dist: pandas
Requires-Dist: tqdm
Requires-Dist: pyarrow
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Dynamic: license-file

# proGenomes-cli

proGenomes-cli is a command-line tool for exploring the [proGenomes](https://progenomes.embl.de) dataset of bacterial and archaeal genomes.

If you use this software in a publication please cite:

> Fullam, Anthony; Letunic, Ivica,; Maistrenko, Oleksandr; Castro, Alexandre A; Coelho, Luis Pedro; Grekova, Anastasia ; Schudoma, Christian; Khedkar, Supriya; Robbani, Shahriyar Mahdi; Kuhn, Michael; Schmidt, Thomas S. B; Bork, Peer; Mende, Daniel R. **proGenomes4: providing two million accurately and consistently annotated high-quality prokaryotic genomes.** in *Nucleic Acids Research*. (accepted)

## Installation

Clone this repository and install using `pip`:

```bash
pip install .
```

## Usage

After installation, the `progenomes` command provides access to several subcommands:

```bash
progenomes download <options>   # Download genome data
progenomes view <options>       # Inspect downloaded data
```

Refer to the built-in help for full details on available commands.

```bash
progenomes --help
```

## License

This project is licensed under the [MIT License](LICENSE).

