Metadata-Version: 2.1
Name: oakx-oger
Version: 0.1.6
Summary: OGER plugin for oaklib
Author: Harshad Hegde
Author-email: hhegde@lbl.gov
Requires-Python: >=3.9,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Provides-Extra: docs
Requires-Dist: OGER (>=1.5,<2.0)
Requires-Dist: click (>=8.1.7,<9.0.0)
Requires-Dist: importlib (>=1.0.4,<2.0.0)
Requires-Dist: oaklib (>=0.5.19)
Description-Content-Type: text/markdown

# oakx-oger

This is an [OGER](https://github.com/OntoGene/OGER) plugin for [`oaklib`](https://github.com/INCATools/ontology-access-kit).

**ALPHA**

## Usage

```
pip install oakx-oger
runoak -i oger:sqlite:obo:envo annotate cultured organisms polar ecosystems atmospheric gas exchange
```

## How it works

There are two possible inputs to this plugin:
1. A `.txt` file [`runoak -i oger:sqlite:obo:envo annotate --text-file text.txt`]
2. Words that need to be annotated.[`runoak -i oger:sqlite:obo:envo annotate cultured organisms polar ecosystems atmospheric gas exchange`]

Input ontologies generally used `oaklib` can be used with an `oger:` prefix.
Note: This has been tested only with `oger:sqlite:obo:*` for now.


## Acknowledgements

This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [oakx-plugin-cookiecutter](https://github.com/INCATools/oakx-plugin-cookiecutter) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).

