https://github.com/guma44/ushuffle
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README.rst
uShuffle
========
.. image:: https://img.shields.io/pypi/v/ushuffle.svg
:target: https://pypi.python.org/pypi/ushuffle
A Cython wrapper around uShuffle - a useful tool for shuffling biological sequences while preserving the k-let counts
This is just a bundle of files downloaded from `ushuffle <http://digital.cs.usu.edu/~mjiang/ushuffle/>`_
and wrapped in Cython for easy installation and use.
Installation
------------
.. code-block :: bash
git clone https://github.com/guma44/ushuffle.git
cd ushuffle
python setup.py install [ --user ]
or
.. code-block :: bash
pip install [--user] ushuffle
Usage
-----
The library exposes a shuffling function shuffle and a Shuffler object used to
make shuffling many times eg.:
.. code-block :: python
from ushuffle import shuffle, Shuffler
seq = "ababcdcdabdcabvababab"
shuffler = Shuffler(seq, 2)
for i in range(10):
seqres = shuffler.shuffle()
print("results:", seqres)
print shuffle(seq, 2)
References
----------
If you use this tool please refer to the original paper and authors:
Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne. `uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. <http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-192>`_ BMC Bioinformatics, 9:#192, 2008.