[Bioperl-l] Bio::Location::Split question

Chris Fields cjfields at uiuc.edu
Thu Sep 21 16:43:27 EDT 2006


Hilmar,

Here's a question which I can't quite find the answer for.  The current
behavior of Bio::Location::Split is to propagate strand information (using
$loc->strand()) for a Split location object to the various sublocations it
contains.  In other words, it isn't just a get/set, but has a direct effect
on the sublocation objects and assumes that all sublocations have the same
strand as the Split location container object.  Would you know of any
rationale for this?  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Monday, September 18, 2006 5:27 PM
> To: Chris Fields
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::Location::Split question
> 
> On Sep 18, 2006, at 5:55 PM, Chris Fields wrote:
> 
> > However, if I take the two examples above, run them through
> > FTLocationFactory, then use to_FTstring() to get the feature
> > string, this is
> > what I get:
> >
> > complement(join(2691..4571,4918..5163))
> >
> > complement(join(4918..5163,2691..4571))
> 
> So this looks like a bug, right? The correct result would be if both
> yielded the same strings, or syntactically equivalent strings. The
> two above are neither identical nor syntactically equivalent.
> 
> Another test is if you set a feature location from either string and
> then request the sub-sequence, the resulting sequence should be
> identical given syntactically equivalent location specifications.
> 
> Do you want to file (and possibly address?) this?
> 
> 	-hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
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