[Bioperl-l] (no subject)

[Heikki Lehvaslaiho]

Xiawu,


You've been caught by what I think is the most common newby problem in
sequence retrieval. Entries with NT_ accession numbers are not GenBank
entries at all. They just follow GenBank entry format. In fact, they are
RefSeq entries and can not be found from the same place. 

You need to use Bio::DB::RefSeq module to retrieve them. Also, you could
take a look at Bio::Perl::get_sequence() where this logic is built in. I
think these modules are only in CVS at this point, definitely not on 0.7
releases.

	-Heikki

 

On Fri, 2002-02-08 at 21:16, Xiaowu Gai wrote:
> Hi All:
> 
> I am using BioPerl in my project and I found something that was really 
> puzzling, I am not very sure it is a bug though:
> 
> When I tried to use the get_Seq_by_acc method, it failed with the error 
> message "Can not call method "_generic_seqfeature" on an undefined value at 
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm line 272". 
> However, it only gave me such error when I tried to get the sequence with 
> the accession number of NT_006204 which is a big big sequence, and it 
> worked just fine if I use another accession number such as AI770588 which 
> is a short EST sequence. Can someone help me here? Thank you so much.
> 
> Here is the codes that I used to test it:
> 
> use Bio::DB::GenBank;
> use Bio::Seq;
> 
> my $gb = new Bio::DB::GenBank();
> my $seq = $gb->get_Seq_by_acc("NT_006204");    # does not work
>          or
> my $seq = $gb->get_Seq_by_acc("AI770588");      # does work
> print $seq->desc();
> 
> Have a nice day.
> 
> Xiaowu
> 
> 
> Xiaowu Gai, PhD
> Associate Scientist
> L. H. Baker Center for Bioinformatics and Biostatistics
> Iowa State University
> Ames, IA 50011
> Phone: (515) 294-7624
> Email: xgai@iastate.edu
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________