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.. 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 --input <input seq file> --output-csv <output csv file>
The input can be a FASTA file, a GenBank file, or a FASTQ file. This can be GZipped or uncompressed.
It can also be a URL.
This will output all the predictions in a CSV file.
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-tools --help
.. end-quickstart
Credits
==================================
* `Robert Turnbull <https://robturnbull.com>`_
* VinÃcius Salazar
* Edoardo Tescari
* Heroen Verbruggen
With contributions from:
* Yuhao Tong
* Kamalpreet Singh
* Rafsan Al Mamun
* Diego Aranda Villarreal
Citation details to come.
* Created using torchapp (https://github.com/rbturnbull/torchapp)
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