skbio.sequence.Sequence.match_frequency

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

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

State: Stable as of 0.4.0.

Parameters

  • other (str, Sequence, or 1D np.ndarray (np.uint8 or '|S1')) – Sequence to compare to.

  • relative (bool, optional) – If True, return the relative frequency of matches instead of the count.

Returns

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.

Return type

int or float

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