[Biopython] define circular DNA (?)

[Peter Cherepanov]

I suppose if a DNA sequence is kept as a simple Python string, there is no easy way to have it "circular". I am a beginner in Python (I use it only occasionally, to solve very specific and simple-minded tasks, when manual match/cut-and-paste operations become too much of a burden). Having spent an extra hour to hack out and debug a piece of code to match/extract to/from circular plasmid sequences kept as Python strings, I thought: hey, wait a minute, there is such thing as BioPython, which should have made this task so much easier... 

Is there a way to "enhance" the Seq object? (or may be I do not know what I am talking about...). 

thanks a lot for responding!

with best wishes, 

Peter


On 8 Mar 2011, at 08:45, Peter Cock wrote:

> On Tue, Mar 8, 2011 at 2:42 AM, Peter Cherepanov wrote:
>> is there an easy way to define a circular DNA sequence in BioPython?
>> 
>> It would be useful to have something like:
>> 
>> my_seq = Seq('ATGCATGC...ATGC', circular_dna)
>> 
>> am I missing something obvious??
>> 
>> Peter
> 
> No, but how would you expect it to act? We've talked
> about such an object before... I'd have to go though my
> old emails but I recall there being some annoying corner
> cases to consider with the slice method (__getitem__).
> 
> Peter