skbio.sequence.distance.kmer_distance

skbio.sequence.distance.kmer_distance(seq1, seq2, k, overlap=True)

Compute the kmer distance between a pair of sequences.

The kmer distance between two sequences is the fraction of kmers that are unique to either sequence.

Parameters:

seq1, seq2Sequence

Sequences to compute kmer distance between.

kint

The kmer length.

overlapbool, optional

Defines whether the kmers should be overlapping or not.

Returns:

float

kmer distance between seq1 and seq2.

Raises:

ValueError

If k is less than 1.

TypeError

If seq1 and seq2 are not Sequence instances.

TypeError

If seq1 and seq2 are not the same type.

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) 
0.9230769230...