How to extract short sequence based on step size?

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The code below extract short sequence in every sequence with the window size 100. The window will shift by step size one and extract the sequence. I would like to extract the short sequence with every step size 50. Can anyone help me?

 from Bio import SeqIO

 with open("B.fasta","w") as f:
         for seq_record in SeqIO.parse("A.fasta", "fasta"):
             for i in range(len(seq_record.seq) - 99) :
                f.write(str(">"+seq_record.id) + "\n")
                f.write(str(seq_record.seq[i:i+100]) + "\n")

Example of fasta file:

>hg17_ct_ER_ER_142
CTAAAAAAGTAAAAAAGAAAAAAAGAGAAAGAAAGAATATAGAAGCAACAAGTGTAGATTTACATTCTATTAGACAGTGACCCATTAGACCCGGACAAGGGG

Example output:

>hg17_ct_ER_ER_142
CTAAAAAAGTAAAAAAGAAAAAAAGAGAAAGAAAGAATATAGAAGCAACAAGTGTAGATTTACATTCTATTAGACAGTGACCCATTAGACCCGGACAAGG
>hg17_ct_ER_ER_142
TAAAAAAGTAAAAAAGAAAAAAAGAGAAAGAAAGAATATAGAAGCAACAAGTGTAGATTTACATTCTATTAGACAGTGACCCATTAGACCCGGACAAGGG
>hg17_ct_ER_ER_142
AAAAAAGTAAAAAAGAAAAAAAGAGAAAGAAAGAATATAGAAGCAACAAGTGTAGATTTACATTCTATTAGACAGTGACCCATTAGACCCGGACAAGGGG

Expected output:

>hg17_ct_ER_ER_142
CTAAAAAAGTAAAAAAGAAAAAAAGAGAAAGAAAGAATATAGAAGCAACA
>hg17_ct_ER_ER_142
AGTGTAGATTTACATTCTATTAGACAGTGACCCATTAGACCCGGACAAGG
1

There are 1 answers

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heathobrien On

Just use the step size option to the range function:

for i in range(0, len(seq_record.seq) - 99, 50) :