[Bioperl-l] retrieving top_SeqFeatures for RefSeq proteins fails

Eleni Rapsomaniki e.rapsomaniki at mail.cryst.bbk.ac.uk
Tue Apr 11 03:30:38 EDT 2006


Hi again,

Thank you for your reply regarding the retrieval of sequence features for
Refseq proteins. I have updated to bioperl 1.5 but the re-direct still does not
work and the following code:

my $factory = Bio::DB::GenBank->new(-no_redirect => 1);
my $seq = $factory->get_Seq_by_acc(' NM_001008292');

returns:
MSG: [gb| NM_001008292] is not a normal sequence entry but a RefSeq entry.
Redirecting the request.

-------------------- WARNING ---------------------
MSG: acc (gb| NM_001008292) does not exist
---------------------------------------------------

I get the same error when I replace Bio::DB::GenBank with Bio::DB::RefSeq, and
with many other refseq accessions.

Could I be doing something wrong or maybe I should be using a different method
for parsing refseq records? I suppose the alternative is to create objects from
files after fetching them..

Many thanks
Eleni Rapsomaniki



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