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

[Chris Fields]

Yes, that's essentially what I have working now.  I suppose the best way to do this is have an optional type supplied and splice only those, checking the subfeatures to ensure that type exists.  I'll check against SeqFeatureI's spliced_seq() to see if there are any API issues.

chris

On Mar 22, 2010, at 3:26 PM, Jason Stajich wrote:

> 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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>> 
> 
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