[Bioperl-l] get sequence failure

[Sebastien Moretti]

Hi,
I use 
	use Bio::DB::GenBank;
	use Bio::DB::Query::GenBank;
	use Bio::SeqIO;
and I can get RefSeq, nr and GenPept files with accession numbers.

> 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!!

-- 
Sebastien MORETTI
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex 20, FRANCE
tel. +334 91 16 44 55 - +336 61 88 59 00