[Bioperl-l] additional methods for Bio::SeqUtils for in-silico cloning

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu Jan 19 15:45:25 EST 2012


Just to throw a spanner in the works, how do we deal with circular features?
I'm guessing an "is_circular" flag somewhere then negative cords might be useful?
Is that what Lincoln did? I think there was a move to allow Gbrowse to handle circular features but don't recall the details.

--Russell


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Fields, Christopher J
> Sent: Friday, 20 January 2012 4:40 a.m.
> To: Roy Chaudhuri
> Cc: Frank Schwach; <bioperl-l at bioperl.org>
> Subject: Re: [Bioperl-l] additional methods for Bio::SeqUtils for in-silico
> cloning
> 
> On Jan 19, 2012, at 9:15 AM, Roy Chaudhuri wrote:
> 
> > I'm not sure I understand the problem with "<1", < means "less than" not
> "less than or equal to", so it does not imply that the feature could start at
> position 1.
> 
> Yup, that's correct.  My bad.
> 
> > I can see that there would be cases where negative coordinates might be
> useful, but I think it is opening a can of worms and could introduce many
> subtle bugs, so I'd vote for throwing an error. If you were to do it, it would be
> better to stick with the biological convention of -1 being the base before 1 (as
> used for -10 and -35 elements).
> >
> > Roy.
> 
> Agree with Roy, I think it's best to avoid using negative cords when at all
> possible, mainly b/c it introduces possibly inconsistent behavior.  Such
> behavior should be defined in the feature class or its parent class(es),
> wherever appropriate.  At the moment that doesn't hold true.
> 
> As a side note, I recall Lincoln allowed negative coords with GBrowse
> features but I don't recall whether it's officially supported.
> 
> chris
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