[Bioperl-l] get sequence failure

[Andrew Walsh]

Hi,

I think the problem could be that you are trying to retrieve a contig 
(NT number). I remember Bio::DB::GenBank used to have problems with 
those, but I'm not sure about now.

And from reading the Bio::Perl::get_sequence POD, I see:

         get_sequence

         Title   : get_sequence
         Usage   : $seq_object = get_sequence('swiss',"ROA1_HUMAN");
...

         Args    : database type - one of swiss, embl, genbank or refseq
                   identifier or accession number


Are you sure 'nr' is a valid database type?

Cheers,

Andrew



william ritchie wrote:
> Hi,
> 
> I m trying to retrieve a sequence with the following
> code:
> 
> use Bio::SearchIO;
> use Bio::Perl;
> use Bio::SeqIO;
> 
> my $seq_object = get_sequence("nr","NT_039208.2");
> 
> and I m getting this error:
> 
> MSG: id does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_id
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:155
> STACK Bio::Perl::get_sequence
> /usr/lib/perl5/site_perl/5.8.0/Bio/Perl.pm:513
> STACK toplevel getseq.pl:9
> 
> this ID does exist, using the ncbi interface I can
> retrieve it!
> Help!!!!Please!!
> 
> 
> 
> 	
> 
> 	
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Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
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