skbio.sequence.distance.
kmer_distance
(seq1, seq2, k, overlap=True)[source]¶Compute the kmer distance between a pair of sequences
State: Experimental as of 0.5.0.
The kmer distance between two sequences is the fraction of kmers that are unique to either sequence.
Parameters: |
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Returns: | kmer distance between seq1 and seq2. |
Return type: | float |
Raises: |
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Notes
kmer counts are not incorporated in this distance metric.
np.nan
will be returned if there are no kmers defined for the
sequences.
Examples
>>> from skbio import Sequence
>>> seq1 = Sequence('ATCGGCGAT')
>>> seq2 = Sequence('GCAGATGTG')
>>> kmer_distance(seq1, seq2, 3) # doctest: +ELLIPSIS
0.9230769230...