PyCoMSA |Stars|
===============

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*Cython bindings and Python interface to* `CoMSA <https://github.com/refresh-bio/CoMSA/>`_,
*a compressor for multiple sequence alignments*.

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Overview
--------

PyCoMSA is a Python module that provides bindings to Prodigal using
`Cython <https://cython.org/>`_. It directly interacts with the CoMSA
internals, which has the following advantages:


.. grid:: 1 2 3 3
   :gutter: 1

   .. grid-item-card:: :fas:`battery-full` Batteries-included

      Just add ``pycomsa`` as a ``pip`` or ``conda`` dependency, no need
      for the CoMSA binary or any external dependency.

   .. grid-item-card:: :fas:`screwdriver-wrench` Sans I/O

      Build alignments to compress as Python `str` or byte-like objects, no 
      need for intermediate files.

   .. grid-item-card:: :fas:`text-slash` Flexible format
      
      Pick the file format based on your needs, and not based on the 
      file format of the original aligmnment.

   .. grid-item-card:: :fas:`arrow-right-arrow-left` Better portability

      Support reading and writing files for any architecture, and not
      just native one as the original CoMSA.

   .. grid-item-card:: :fas:`check` Compatible

      Load files generated with PyCoMSA using CoMSA, as both are using 
      the same compression method.

   .. grid-item-card:: :fas:`toolbox` Feature-complete

      Access all the features of the original CLI through the :doc:`Python API <api/index>`.



Setup
-----

Run ``pip install pycomsa`` in a shell to download the latest release and all
its dependencies from PyPi, or have a look at the
:doc:`Installation page <guide/install>` to find other ways to install 
``pycomsa``.


Library
-------

Check the following pages of the user guide or the API reference for more
in-depth reference about library setup, usage, and rationale:

.. toctree::
   :maxdepth: 2

   User Guide <guide/index>
   API Reference <api/index>


Related Projects
----------------

The following Python libraries may be of interest for bioinformaticians.

.. include:: related.rst


License
-------

This library is provided under the `GNU General Public License v3.0 <https://choosealicense.com/licenses/gpl-3.0/>`_.
The Prodigal code was written by `Sebastian Deorowicz <https://github.com/sebastiandeorowicz>`_ and is distributed under the
terms of the GPLv3 as well. See the :doc:`Copyright Notice <guide/copyright>` section
for the full GPLv3 license.

*This project is in no way not affiliated, sponsored, or otherwise endorsed by
the original* `Prodigal`_ *authors. It was developed by* `Martin Larralde <https://github.com/althonos>`_ 
*during his PhD project at the* `Leiden University Medical Center <https://www.lumc.nl/en/>`_
*in the* `Zeller team <https://github.com/zellerlab>`_.