skbio.sequence.Sequence.distance#
- Sequence.distance(other, metric=None)[source]#
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 aSequence
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.- metriccallable, optional
Function used to compute the distance between this sequence and
other
. By default, Hamming distance will be used (seehamming
).metric
should be a function that takes twoSequence
objects and returns afloat
. The sequence objects passed tometric
will be the same type as this sequence. Seeskbio.sequence.distance
for other predefined metrics that can be supplied viametric
.
- Returns:
- float
Distance between this and other sequences as defined by
metric
.
- Raises:
- TypeError
If
other
is aSequence
object with a different type than this sequence.
See also
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