skbio.sequence.Sequence.match_frequency#

Sequence.match_frequency(other, relative=False)[source]#

Return count of positions that are the same between two sequences.

Parameters:

otherstr, Sequence, or 1D np.ndarray (np.uint8 or ‘|S1’): Sequence to compare to.
relativebool, optional: If True, return the relative frequency of matches instead of the count.

Returns:

int or float: Number of positions that are the same between the sequences. This will be an int if relative is False and a float if relative is True.

Raises:

ValueError: If the sequences are not the same length.
TypeError: If other is a Sequence object with a different type than this sequence.

See also

mismatch_frequency
matches
mismatches
distance

Examples

>>> from skbio import Sequence
>>> s = Sequence('GGUC')
>>> t = Sequence('AGUC')
>>> s.match_frequency(t)
3
>>> s.match_frequency(t, relative=True)
0.75