skbio.sequence.DNA.distance

DNA.distance(other, metric=None)[source]

Compute the distance to another sequence.

State: Experimental as of 0.4.0.

Parameters:

  • other (str, Sequence, or 1D np.ndarray (np.uint8 or '|S1')) – Sequence to compute the distance to. If other is a Sequence object, it must be the same type as this sequence. Other input types will be converted into a Sequence object of the same type as this sequence.

  • metric (function, optional) – Function used to compute the distance between this sequence and other. If None (the default), Hamming distance will be used (skbio.sequence.distance.hamming()). metric should take two skbio.Sequence objects and return a float. The sequence objects passed to metric will be the same type as this sequence. See skbio.sequence.distance for other predefined metrics that can be supplied via metric.

Returns:

Distance between this sequence and other as defined by metric.

Return type:

float

Raises:

TypeError – If other is a Sequence object with a different type than this sequence.

See also

skbio.sequence.distance, fraction_diff, fraction_same

Examples

>>> from skbio import Sequence
>>> s = Sequence('GGUC')
>>> t = Sequence('AGUC')

Compute Hamming distance (the default metric):

>>> s.distance(t)
0.25

Use a custom metric:

>>> def custom_metric(s1, s2): return 0.42
>>> s.distance(t, custom_metric)
0.42