skbio.sequence.Sequence.distance

Sequence.distance(other, metric=None)

Compute the distance to another sequence.

Parameters:

otherstr, 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.

metricfunction, 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:

float

Distance between this sequence and other as defined by metric.

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