[Bioperl-l] Bio::DB::SeqFeature spliced_seq()

[Jason Stajich]

Yes it needs a special case I guess - since spliced_seq should work, 
however ...  The only problem is that if both exons and CDS are 
sub-features you have to be smart enough to not grab both...

So I have just relied on specialized dumping scripts for gff3_to_cds for 
my own needs (i.e. 
http://github.com/hyphaltip/genome-scripts/blob/master/seqfeature/dbgff_to_cdspep.pl 
).
But you might also see what the Gbrowse plugin dumpers do.

-jason
Chris Fields wrote, On 3/22/10 11:56 AM:
> I have just noticed that spliced_seq() is borked with
> Bio::DB::SeqFeature and am thinking about implementing it.  Or is
> similar functionality already implemented elsewhere?
>
> Currently, it is calling entire_seq(), which I plan on avoiding simply
> to prevent sucking in the entire sequence into memory.  This is
> currently what happens:
>
> <partial code>
> ---------------------------
>
> my $it = $store->get_seq_stream(-type =>  'mRNA');
>
> my $ct = 0;
> while (my $sf = $it->next_seq) {
>      my $seq = $sf->spliced_seq;  # dies with exception
> }
>
> ---------------------------
>
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Abstract method "Bio::SeqFeatureI::entire_seq" is not implemented
> by package Bio::DB::SeqFeature.
> This is not your fault - author of Bio::DB::SeqFeature should be blamed!
>
> STACK: Error::throw
> STACK:
> Bio::Root::Root::throw /home/cjfields/bioperl/live/Bio/Root/Root.pm:368
> STACK:
> Bio::Root::RootI::throw_not_implemented /home/cjfields/bioperl/live/Bio/Root/RootI.pm:739
> STACK:
> Bio::SeqFeatureI::entire_seq /home/cjfields/bioperl/live/Bio/SeqFeatureI.pm:325
> STACK:
> Bio::SeqFeatureI::spliced_seq /home/cjfields/bioperl/live/Bio/SeqFeatureI.pm:458
> STACK: beestore.pl:17
> ----------------------------------------------------------------
>
>
>
> chris
>
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