skbio.sequence.GrammaredSequence.mismatch_frequency¶

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

Return count of positions that differ between two sequences.

State: Stable as of 0.4.0.

Parameters:

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:	int or float Number of positions that differ 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.

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:

int or float

Number of positions that differ 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.

Examples

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