[Bioperl-l] get sequence failure

[Jason Stajich]

You need to use 'refseq' as the db type for refseq sequences ("NT", "NM")

'nr' is not a recognized type of seq db in the first place anyways...

I'm noticing for the documentation and code that the types are really
documented very well for get_sequence -- need someone to fix this please.

-jason

On Mon, 16 Feb 2004, [iso-8859-1] 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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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu