ushuffle python example

ushuffle_example.py

# ref: https://github.com/guma44/ushuffle
# ref: https://www.python.org/dev/peps/pep-3112/
# ref: https://pypi.org/project/ushuffle/

from ushuffle import shuffle, Shuffler, set_seed

set_seed(12345)

seq = bytes('ATTTTCTTTTTTTTTTA', 'ascii')

# Note: '2' indicates that the shuffled sequence preserves 2-mer frequency
print(shuffle(seq, 2))



# Repeat shuffling
shuffler = Shuffler(seq, 2)
for i in range(10):
    seqres = shuffler.shuffle()
    print("results:", seqres)

>>> from ushuffle import shuffle, Shuffler, set_seed
>>> seq = bytes('ATTTTCTTTTTTTTTTA', 'ascii')
>>>
>>> # Note: '2' indicates that the shuffled sequence preserves 2-mer frequency
... print(shuffle(seq, 2))
b'ATTTTTTCTTTTTTTTA'
>>>
>>>
>>>
>>> # Repeat shuffling
... shuffler = Shuffler(seq, 2)
>>> for i in range(10):
...     seqres = shuffler.shuffle()
...     print("results:", seqres)
...
results: b'ATTTTTTTTTCTTTTTA'
results: b'ATTTTCTTTTTTTTTTA'
results: b'ATTTTTTTCTTTTTTTA'
results: b'ATTTTTTTTTTTCTTTA'
results: b'ATCTTTTTTTTTTTTTA'
results: b'ATTTTTTTTTTTTTCTA'
results: b'ATTTTTCTTTTTTTTTA'
results: b'ATTTTTTTTCTTTTTTA'
results: b'ATTTTTTTTTTTTCTTA'
results: b'ATTCTTTTTTTTTTTTA'

>>> seq = bytes('KTTTTCTTTTTTTTTTA', 'ascii')
>>>
>>> # Note: '2' indicates that the shuffled sequence preserves 2-mer frequency
... print(shuffle(seq, 2))
b'KTTTTTTTTTTCTTTTA'
>>>
>>>
>>>
>>> # Repeat shuffling
... shuffler = Shuffler(seq, 2)
>>> for i in range(10):
...     seqres = shuffler.shuffle()
...     print("results:", seqres)
...
results: b'KTTTTTTTCTTTTTTTA'
results: b'KTTTTTTTTTTTCTTTA'
results: b'KTTTTTTTTTTTTCTTA'
results: b'KTTCTTTTTTTTTTTTA'
results: b'KTTTTTTTTTTTTCTTA'
results: b'KTTCTTTTTTTTTTTTA'
results: b'KTTTTTTTTTTTCTTTA'
results: b'KTTTTTTTTCTTTTTTA'
results: b'KTTTTTTTTTTTTTCTA'
results: b'KTTTTTTTTTTCTTTTA'