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.

Python 2:

.. 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)

Python 3:

.. code-block :: python

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

The library exposes also the function to set the random seed called set_seed. This sets the seed globally once and subsequent call to this function will not change the seed anymore.

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.