skbio.sequence.Sequence.find_with_regex#

Sequence.find_with_regex(regex, ignore=None)[source]#

Generate slices for patterns matched by a regular expression.

Parameters:

regexstr or regular expression object: String to be compiled into a regular expression, or a pre- compiled regular expression object (e.g., from calling re.compile).
ignore1D array_like (bool) or iterable (slices or ints), optional: Indicate the positions to ignore when matching.

Yields:

slice: Location where the regular expression matched.

Examples

>>> from skbio import Sequence
>>> s = Sequence('AATATACCGGTTATAA')
>>> for match in s.find_with_regex('(TATA+)'):
...     match
...     str(s[match])
slice(2, 6, None)
'TATA'
slice(11, 16, None)
'TATAA'