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] ushuffleUsage
The library exposes a shuffling function shuffle and a Shuffler object used to make shuffling many times.
Python 2:
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:
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. BMC Bioinformatics, 9:#192, 2008.
1 maintainer
Metadata
1 maintainer
Release files for ushuffle 1.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ushuffle-1.1.2.tar.gz | 35.1 kB | Details |
Release files / ushuffle-1.1.2.tar.gz
| Download URL | ushuffle-1.1.2.tar.gz |
|---|---|
| Size | 35.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
bd2c1d038a6d67d5a0c9f3e0b1761dccd9400bde666c82bb8f44732b72d417b6
|
|
BLAKE2b-256 checksum How to use checksums |
a24c96ca5e83e53e834e82bdb0d1e325e4fc1a165a08296e1d0fec6b32d3dbb0
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.45.0 CPython/3.7.4
|
