[BioPython] help for searching overlapping occurrences
Jeffrey Chang
jchang at jeffchang.com
Wed Oct 22 13:47:07 EDT 2003
On Wednesday, October 22, 2003, at 11:58 AM, Andrew Dalke wrote:
> Jeff:
>> 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
>
> Consider the pattern
>
> a(bc|bcd)
>
> when searched against
>
> abcd
Yes, that would indeed fail.
Alessandro, can you tell us more about your problem? I suspect you may
be searching for occurrences of a motif, such as GA.CC, within a DNA
sequence. If so, you may not need exactly what you said you needed...
Jeff
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