easy method for spliting substrings of a given length from a string

Question

I have a 34-mer string like

ATGGGGTTTCCC...CTG

I want to get all possible 6-mer substrings in this string. Can you suggest a good way to do this.

Quite close stackoverflow.com/questions/21303224/… though not an exact dupe — Bhargav Rao
– Bhargav Rao, Commented Jun 10, 2015 at 18:12

Cory Kramer · Accepted Answer · 2015-06-10 18:15:01Z

1

Assuming they have to be contiguous, you can use slicing in a list comprehension

>>> s = 'AGTAATGGCGATTGAGGGTCCACTGTCCTGGTAC'
>>> [s[i:i+6] for i in range(len(s)-5)]
['AGTAAT', 'GTAATG', 'TAATGG', 'AATGGC', 'ATGGCG', 'TGGCGA', 'GGCGAT', 'GCGATT', 'CGATTG', 'GATTGA', 'ATTGAG', 'TTGAGG', 'TGAGGG', 'GAGGGT', 'AGGGTC', 'GGGTCC', 'GGTCCA', 'GTCCAC', 'TCCACT', 'CCACTG', 'CACTGT', 'ACTGTC', 'CTGTCC', 'TGTCCT', 'GTCCTG', 'TCCTGG', 'CCTGGT', 'CTGGTA', 'TGGTAC']

answered Jun 10, 2015 at 18:15

Cory Kramer

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