skbio.sequence.distance.
hamming
(seq1, seq2)[source]¶Compute Hamming distance between two sequences.
State: Experimental as of 0.4.2.
The Hamming distance between two equal-length sequences is the proportion of differing characters.
Parameters: | seq1, seq2 : Sequence
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Returns: | float
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Raises: | TypeError
TypeError
ValueError
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See also
scipy.spatial.distance.hamming
Notes
np.nan
will be returned if the sequences do not contain any characters.
This function does not make assumptions about the sequence alphabet in use. Each sequence object’s underlying sequence of characters are used to compute Hamming distance. Characters that may be considered equivalent in certain contexts (e.g., - and . as gap characters) are treated as distinct characters when computing Hamming distance.
Examples
>>> from skbio import Sequence
>>> from skbio.sequence.distance import hamming
>>> seq1 = Sequence('AGGGTA')
>>> seq2 = Sequence('CGTTTA')
>>> hamming(seq1, seq2)
0.5