Metadata-Version: 2.1
Name: bio-corgi
Version: 0.4.0
Summary: Classifier for ORganelle Genomes Inter alia
Home-page: https://github.com/rbturnbull/corgi
License: Apache Software License 2.0
Keywords: metagenomic classifier,tiara,DNA,bioinformatics,fastai,pytorch,deep learning,command-line interface
Author: Robert Turnbull
Author-email: robert.turnbull@unimelb.edu.au
Requires-Python: >=3.8,<3.12
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
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Requires-Dist: beautifulsoup4 (>=4.10.0,<5.0.0)
Requires-Dist: biopython (>=1.79,<2.0)
Requires-Dist: cryptography (>=36.0.1,<37.0.0)
Requires-Dist: dask (>=2021.7.1,<2022.0.0)
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Requires-Dist: torchapp (>=0.3.1)
Requires-Dist: wandb (>=0.12.9,<0.13.0)
Project-URL: Documentation, https://rbturnbull.github.io/corgi/
Project-URL: Repository, https://github.com/rbturnbull/corgi
Description-Content-Type: text/x-rst

.. image:: https://raw.githubusercontent.com/rbturnbull/corgi/main/docs/images/corgi-banner.svg

.. start-badges

|testing badge| |coverage badge| |docs badge| |black badge| |git3moji badge| |torchapp badge|

.. |testing badge| image:: https://github.com/rbturnbull/corgi/actions/workflows/testing.yml/badge.svg
    :target: https://github.com/rbturnbull/corgi/actions

.. |docs badge| image:: https://github.com/rbturnbull/corgi/actions/workflows/docs.yml/badge.svg
    :target: https://rbturnbull.github.io/corgi
    
.. |black badge| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black
    
.. |coverage badge| image:: https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/rbturnbull/ee1b52dd314d6441e0aabc0e1e50dc2c/raw/coverage-badge.json
    :target: https://rbturnbull.github.io/corgi/coverage/

.. |git3moji badge| image:: https://img.shields.io/badge/git3moji-%E2%9A%A1%EF%B8%8F%F0%9F%90%9B%F0%9F%93%BA%F0%9F%91%AE%F0%9F%94%A4-fffad8.svg
    :target: https://robinpokorny.github.io/git3moji/

.. |torchapp badge| image:: https://img.shields.io/badge/MLOpps-torchapp-B1230A.svg
    :target: https://rbturnbull.github.io/torchapp/
        
.. end-badges

.. start-quickstart

Installation
============

The software can be installed using ``pip``

.. code-block:: bash

    pip install bio-corgi

.. warning ::

    Do not try just `pip install corgi` because that is a different package.

To install the latest version from the repository, you can use this command:

.. code-block:: bash

    pip install git+https://github.com/rbturnbull/corgi.git

.. note ::

    Soon corgi will be able to be installed using conda.


Usage
============

To make predictions, run the ``corgi`` command line tool:

.. code-block:: bash

    corgi --file <input seq file>

This will create a directory with the predictions in a CSV file and in fasta format.

For more information about the other options, see the help with:

.. code-block:: bash

    corgi --help

For help on training a model with corgi, run:

.. code-block:: bash

    corgi-train --help


.. end-quickstart


Credits
==================================

* Robert Turnbull <robert.turnbull@unimelb.edu.au>
* Created using torchapp (https://github.com/rbturnbull/torchapp)


