In [1]:

    

from miRNAlearnIO import fasta_iter
mirnas = [s for t,s in fasta_iter('examples/csec_mirbase.fa')]
print(len(mirnas))


    

    




320

In [2]:

    

!seq_shuffler/altschulEriksonDinuclShuffle.py


    

    




Usage: %s RNAsequence

In [3]:

    

shuffled = list()
for rna in mirnas:
    seq = rna.replace('T', 'U').replace('t', 'u')
    shuffled_seq = !seq_shuffler/altschulEriksonDinuclShuffle.py $seq
    shuffled.append(shuffled_seq[0])


    

In [4]:

    

print(len(shuffled))


    

    




320

In [5]:

    

labels = [t for t,s in fasta_iter('examples/csec_mirbase.fa')]

with open('examples/csec_mirbase_shuffled.fa', 'w') as of:
    for i,seq in enumerate(shuffled):
        of.write('> shuffled|' + labels[i] + '\n')
        of.write(seq + '\n')


    

In [7]:

    

!wc -l examples/csec_mirbase_shuffled.fa


    

    




     640 examples/csec_mirbase_shuffled.fa

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