skbio.sequence.RNA.distance¶

RNA.
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