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

Mark Johnson johnsonm at gmail.com
Tue Jun 12 12:10:45 EDT 2007


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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