Metadata-Version: 2.4
Name: annocli
Version: 1.0.3
Summary: A command-line tool to query and download genome annotations
Author-email: Fabio Zanarello <fzanarello@crg.eu>
License-Expression: MIT
Project-URL: Homepage, https://github.com/apollo994/annocli
Project-URL: Repository, https://github.com/apollo994/annocli
Project-URL: Documentation, https://github.com/apollo994/annocli/blob/main/USAGE.md
Project-URL: Issues, https://github.com/apollo994/annocli/issues
Keywords: genome,annotation,gff,bioinformatics,annotrieve,cli
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
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: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: requests>=2.25.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: responses>=0.25; extra == "dev"
Dynamic: license-file

# annocli

A command-line tool to query and download genome annotations from the [Annotrieve API](https://genome.crg.es/annotrieve/).

## Installation

```bash
pip install annocli
```

From source:

```bash
git clone https://github.com/apollo994/annocli.git
cd annocli
pip install .
./test.sh
```

For development (includes pytest):

```bash
pip install -e ".[dev]"
```

## Commands

```bash
annocli {COMMAND} --help
```

- [`download`](https://github.com/apollo994/annocli/blob/main/USAGE.md#download-command): Download annotations for given taxonomy IDs
- [`alias`](https://github.com/apollo994/annocli/blob/main/USAGE.md#alias-command): Match sequence IDs between annotation and assembly files
- [`summary`](https://github.com/apollo994/annocli/blob/main/USAGE.md#summary-command): Get information about features and biotypes available
- [`stats`](https://github.com/apollo994/annocli/blob/main/USAGE.md#stats-command): Get summary statistics about gene and transcript features

For detailed usage examples, see [USAGE.md](https://github.com/apollo994/annocli/blob/main/USAGE.md).

## Testing

Unit and component tests (mocked, no network):

```bash
pytest
```

End-to-end tests against the live Annotrieve API:

```bash
pytest -m e2e
```
