skbio.sequence.GrammaredSequence.index

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

Find position where subsequence first occurs in the sequence.

State: Stable as of 0.4.0.

Parameters

  • subsequence (str, Sequence, or 1D np.ndarray (np.uint8 or '|S1')) – Subsequence to search for in this sequence.

  • start (int, optional) – The position at which to start searching (inclusive).

  • end (int, optional) – The position at which to stop searching (exclusive).

Returns

Position where subsequence first occurs in this sequence.

Return type

int

Raises

  • ValueError – If subsequence is not present in this sequence.

  • TypeError – If subsequence is a Sequence object with a different type than this sequence.

Examples

>>> from skbio import Sequence
>>> s = Sequence('ACACGACGTT-')
>>> s.index('ACG')
2