skbio.sequence.Sequence.distance¶
- Sequence.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 aSequence
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 twoskbio.Sequence
objects and return afloat
. The sequence objects passed to metric will be the same type as this sequence. Seeskbio.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:
- 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