[Bioperl-l] Bio::SeqFeature::Gene::Exon throws exception when encountering split location (Bio::Location::Split)

Hilmar Lapp hlapp at gmx.net
Tue Jun 12 20:55:57 EDT 2007


I think it was just trying to guard against people trying to do  
stupid things.

I'm actually not sure that representing locations on a circular  
genome using split locations really is the best thing. I'm wondering  
whether one shouldn't rather introduce a CircularLocation object  
(though obviously it isn't the location that's circular...).

Just a thought. In the end, if you have a way to make this work that  
you feel comfortable with than go for it.

	-hilmar

On Jun 12, 2007, at 12:10 PM, Mark Johnson wrote:

> On 6/12/07, Torsten Seemann  
> <torsten.seemann at infotech.monash.edu.au> wrote:
>> Can you use the ->spliced_seq() method to do this?
>>
>> http://doc.bioperl.org/releases/bioperl-1.5.2/Bio/ 
>> SeqFeatureI.html#POD11
>>
>> --
>> --Torsten Seemann
>> --Victorian Bioinformatics Consortium, Monash University
>> --Tel +61 3 9905 9010
>
>     Actually, I'd forgotten about spliced_seq().  That seems like it
> will Do The Right Thing.  It's just up to the invoker to call
> spliced_seq() instead of seq() as appropriate.
>     So, is there any other code that will break if I modify
> Bio::SeqFeature::Gene::Exon::location to not throw an exception when
> encountering Bio::Location::SplitLocationI?  I'm wondering if it's
> just a paranoid check or if it's there to guard against something.  If
> the latter, I need to know what code to fix.  I'll dig and look, but
> if anybody knows or has an idea, save me some time.  I suppose I can
> just change it and see what tests start failing. 8)
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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