Pyrodigal |Stars|
=================

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*Cython bindings and Python interface to* `Prodigal <https://github.com/hyattpd/Prodigal/>`_,
*an ORF finder for genomes and metagenomes*. **Now with SIMD!**

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Overview
--------

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

- **single dependency**: Pyrodigal is distributed as a Python package, so you
  can add it as a dependency to your project, and stop worrying about the
  Prodigal binary being present on the end-user machine.
- **no intermediate files**: Everything happens in memory, in a Python object
  you fully control, so you don't have to invoke the Prodigal CLI using a
  sub-process and temporary files. Sequences can be passed directly as
  strings or bytes, which avoids the overhead of formatting your input to
  FASTA for Prodigal.
- **lower memory usage**: Pyrodigal is slightly more conservative when it comes
  to using memory, which can help process very large sequences. It also lets
  you save some more memory when running several *meta*-mode analyses
- **better performance**: Pyrodigal uses *SIMD* instructions to compute which
  dynamic programming nodes can be ignored when scoring connections. This can
  save from a third to half the runtime depending on the sequence.

Setup
-----

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


Library
-------

.. toctree::
   :maxdepth: 2

   Installation <install>
   Contributing <contributing>
   Publications <publications>
   Benchmarks <benchmarks>
   API Reference <api/index>
   Changelog <changes>


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 `Doug Hyatt <https://github.com/hyattpd>`_ and is distributed under the
terms of the GPLv3 as well. The ``cpu_features`` library was written by
`Guillaume Chatelet <https://github.com/gchatelet>`_ and is licensed under the terms of the
`Apache License 2.0 <https://choosealicense.com/licenses/apache-2.0/>`_.

*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* `European Molecular Biology Laboratory <https://www.embl.de/>`_
*in the* `Zeller team <https://github.com/zellerlab>`_.