|License: Affero-GPL| || |Platform: C++11 Python3| || |Run on Linux-Mac OSX|

+--------------------+-----------------------+ | MacOSX | Linux | +====================+=======================+ | |Build Status OSX| | |Build Status Ubuntu| | +--------------------+-----------------------+

About pyGATB

pyGATB is a Python3 wrapper for the GATB-Core library <https://github.com/GATB>__.

The current release of pyGATB gives access to the following GATB-Core components:

• Bank: the class that enables to load Fasta and Fastaq files
• Sequence: the class that holds a sequence (ID, letters, quality)
• Graph: the class that holds the De Bruijn graph
• Node: the class that makes graph's nodes

Using that API you can start prototyping algorithms:

• read a sequence file (Bank): FastA, FastQ (plain text or gzipped)
• or read a set of files (still using the same Bank!)
• convert that Bank to a De Bruijn graph (Graph)
• navigate through the Graph (Node)

all of that directly using the Python Programming Language.

Documentation

Jump to the wiki <https://github.com/GATB/pyGATB/wiki>__ to review how to install, use and make pyGATB Python3 compliant codes.

License

pyGATB and GATB-Core are free softwares; you can redistribute it and/or modify it under the Affero GPL v3 license <http://www.gnu.org/licenses/agpl-3.0.en.html>__.

.. |_| unicode:: 0x00A0 :trim: .. |License: Affero-GPL| image:: https://img.shields.io/:license-Affero--GPL-blue.svg :target: https://www.gnu.org/licenses/agpl-3.0.en.html .. |Platform: C++11 Python3| image:: https://img.shields.io/badge/platform-c++/11_Python--3-yellow.svg :target: https://isocpp.org/wiki/faq/cpp11 .. |Run on Linux-Mac OSX| image:: https://img.shields.io/badge/run_on-Linux--Mac_OSX-yellowgreen.svg .. |Build Status OSX| image:: https://ci.inria.fr/gatb-core/view/pyGATB/job/pyGATB-build-macos-10.9.5-gcc-4.2.1/badge/icon :target: https://ci.inria.fr/gatb-core/view/pyGATB/job/pyGATB-build-macos-10.9.5-gcc-4.2.1/ .. |Build Status Ubuntu| image:: https://ci.inria.fr/gatb-core/view/pyGATB/job/pyGATB-build-ubuntu16-gcc-5.4/badge/icon :target: https://ci.inria.fr/gatb-core/view/pyGATB/job/pyGATB-build-ubuntu16-gcc-5.4/