PyNCBItk |Stars|
================

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*Cython bindings and Python interface to the NCBI C++ Toolkit.*

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Overview
--------

The NCBI C++ Toolkit is a framework of C++ libraries to work with biological
sequence data developed at the 
`National Center for Biotechnology Information <https://www.ncbi.nlm.nih.gov/>`_. 
It features a flexible object model for representing sequences of various 
origin, including composite or virtual sequences; a resource manager
to easily manipulate heterogeneous data sources; and a comprehensive API to the
various BLAST algorithms developed at the NBCI.

PyNCBItk is a Python library that provides bindings to the NCBI C++ Toolkit 
data model and BLAST+ interface using `Cython <https://cython.org>`_:

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

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

      Just add ``pyncbitk`` as a ``pip`` or ``conda`` dependency, no need
      for the BLAST+ binaries or any external dependency.

   .. grid-item-card:: :fas:`screwdriver-wrench` Flexible

      Load a `BioSeq` from a :wiki:`FASTA format` file or create 
      it programmatically through the :doc:`Python API <api/index>`.

   .. grid-item-card:: :fas:`gears` Practical

      Retrieve results as they become available as dedicated 
      `SearchResults` objects.


Setup
-----

PyNCBItk is available for all modern Python versions (3.7+).

Run ``pip install pyncbitk`` in a shell to download the latest release from PyPI,
or have a look at the :doc:`Installation page <guide/install>` to find other ways 
to install PyNCBItk.

Library
-------

.. toctree::
   :maxdepth: 2

   User Guide <guide/index>
   Examples <examples/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 `MIT License <https://choosealicense.com/licenses/mit/>`_.
The NCBI C++ Toolkit is a "United States Government Work" and therefore lies in 
the public domain. Some restrictions apply, see the upstream 
`license files <https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/master/doc/public/LICENSE>`_.

*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the NCBI or any associated entity. 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>`_.