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

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Tue Jun 12 02:18:27 EDT 2007


Mark,

> if (ref($self->location()) eq 'Bio::Location::Split')) {
>     my $seqstring;
>     my @sublocs = $self->location()->sub_Location();
>
>     foreach my $subloc (@sublocs) {
>         $seqstring .= $self->{'_gsf_seq'}->trunc($subloc->start(),
> $subloc->end())->seq();
>     }

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


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