ushuffle 1.0.1

A Cython wrapper over uShuffle - a useful tool for shuffling biological sequences while preserving the k-let counts.

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
------------

```
git clone https://github.com/guma44/ushuffle.git
cd ushuffle
python setup.py install [ --user ]
```

or

```
pip install [--user] ushuffle
```

Usage
-----

The library exposes a shuffling function shuffle and a Shuffler object used to
make shuffling many times eg.:

```
from ushuffle import shuffle, Shuffler
seq = "ababcdcdabdcabvababab"
shuffler = Shuffler(self.seq, len(self.seq), 2)
for i in range(10):
seqres = shuffler.shuffle()
print("results:", seqres)
print shuffle(a, 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.