skbio.sequence.Sequence.mismatch_frequency

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

Return count of positions that differ 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 mismatches instead of the count.
Returns:

Number of positions that differ 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

match_frequency(), matches(), mismatches(), distance()

Examples

>>> from skbio import Sequence
>>> s = Sequence('GGUC')
>>> t = Sequence('AGUC')
>>> s.mismatch_frequency(t)
1
>>> s.mismatch_frequency(t, relative=True)
0.25