sequence.py 文件源码

def get_occurences(self, pattern, overlap=False):
        """Return position of the input pattern in the sequence

        ::

            >>> from sequana import Sequence
            >>> s = Sequence('ACGTTTTACGT')
            >>> s.get_occurences("ACGT")
            [0, 7]

        """
        if overlap is False:
            res = [m.start() for m in re.finditer(pattern, self.sequence)]
        elif overlap is True:
            res = [m.start() for m in re.finditer('(?=%s)'%pattern, self.sequence)]
        return res

        # reverse find-all without overlaps, you can combine positive and
        # negative lookahead into an expression like this:
        #res = [m.start() for m in re.finditer('(?=%s)(?!.{1,%d}%s)' % (search,
        #    len(pattern)-1, pattern), 'ttt')]