[BioPython] help for searching overlapping occurrences

[Jeffrey Chang]

On Wednesday, October 22, 2003, at 10:51  AM, Andrew Dalke wrote:

> Alessandro:
>> I' am looking for a method like finditer from module re but
>> returning all the occurrences of a pattern in a straing even
>> if overlapping to each other.
>
> There is no such function.
>
> Such a search may be highly exponential as every ambiguous
> branch must be taken.

Would the following (untested) code do what Alessandro wants?

def finditer_overlapped(pattern, string):
   for i in range(len(string)):
     m = re.match(pattern, string[i:])
     if m:
       yield m

Jeff