[Bioperl-l] Bio::SeqFeature::Gene::Exon throws exception when encountering split location (Bio::Location::Split)
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
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.
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?
>> --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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: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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