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

Chris Fields cjfields at illinois.edu
Mon Mar 22 14:56:30 EDT 2010

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
Bio::Root::Root::throw /home/cjfields/bioperl/live/Bio/Root/Root.pm:368
Bio::Root::RootI::throw_not_implemented /home/cjfields/bioperl/live/Bio/Root/RootI.pm:739
Bio::SeqFeatureI::entire_seq /home/cjfields/bioperl/live/Bio/SeqFeatureI.pm:325
Bio::SeqFeatureI::spliced_seq /home/cjfields/bioperl/live/Bio/SeqFeatureI.pm:458
STACK: beestore.pl:17


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