skbio.sequence.GrammaredSequence.count

GrammaredSequence.count(subsequence, start=None, end=None)[source]

Count occurrences of a subsequence in this sequence.

State: Stable as of 0.4.0.

Parameters:
  • subsequence (str, Sequence, or 1D np.ndarray (np.uint8 or '|S1')) – Subsequence to count occurrences of.
  • start (int, optional) – The position at which to start counting (inclusive).
  • end (int, optional) – The position at which to stop counting (exclusive).
Returns:

Number of occurrences of subsequence in this sequence.
Return type:

int
Raises:
  • ValueError – If subsequence is of length 0.
  • TypeError – If subsequence is a Sequence object with a different type than this sequence.

Examples

>>> from skbio import Sequence
>>> s = Sequence('GGUCG')
>>> s.count('G')
3
>>> s.count('GG')
1
>>> s.count('T')
0
>>> s.count('G', 2, 5)
1