ushuffle 1.0.4

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

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 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(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. BMC Bioinformatics, 9:#192, 2008.