nucleic.sequence module

nucleic.sequence.dna_kmers(k: int = 3) → Generator[[str, None], None]

Return the cartesian product of all DNA substrings of length k.

Parameters:k – Length of of the DNA substring. Yields:Cartesian product of all DNA substrings of length k.

Examples

>>> list(dna_kmers(1))
['A', 'C', 'G', 'T']
>>> len(list(dna_kmers(3)))
64

nucleic.sequence.hamming_circle(string: str, n: int, alphabet: List[str]) → Generator[[str, None], None]

Find strings, of a given alphabet, with a distance of n away from a string.

Examples

>>> sorted(hamming_circle('abc', n=0, alphabet='abc'))
['abc']
>>> sorted(hamming_circle('abc', n=1, alphabet='abc'))
['aac', 'aba', 'abb', 'acc', 'bbc', 'cbc']
>>> sorted(hamming_circle('aaa', n=2, alphabet='ab'))
['abb', 'bab', 'bba']