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Dinucleotide shuffling does not shuffle #136

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swertz opened this issue Nov 15, 2023 · 0 comments
Open

Dinucleotide shuffling does not shuffle #136

swertz opened this issue Nov 15, 2023 · 0 comments

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@swertz
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swertz commented Nov 15, 2023

Hello,

This should be self-explanatory:

from deeplift.dinuc_shuffle import dinuc_shuffle
dinuc_shuffle("ACTGACTGACTG", 20, rng=np.random.default_rng())

Output:

['ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG',
 'ACTGACTGACTG']

Looking at various examples (https://github.com/kundajelab/deeplift/blob/master/examples/genomics/genomics_simulation.ipynb, https://shap.readthedocs.io/en/latest/example_notebooks/genomic_examples/DeepExplainer%20Genomics%20Example.html), it seems this part has been rewritten several times. Alas, the current version does not work. Perhaps this would explain #135 ?
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@swertz