DNA.
distance
(other, metric=None)[source]¶Compute the distance to another sequence.
State: Experimental as of 0.4.0.
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.
Distance between this sequence and other as defined by metric.
float
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