[Bioperl-l] noob Bio::DB::Biblio problem

[Brian Osborne]

Chihiro,

What happens when you set the access mode to "soap" or "eutils" rather than
to "biofetch"?

Brian O.


On 10/31/05 9:19 AM, "Chihiro Yamada" <cy200 at gen.cam.ac.uk> wrote:

> Hiya folks,
> 
> I'm trying to use the Bio::DB::Biblio::biofetch module to get references
> by ID, but I'm having a problem...
> 
> If I run this code...
> 
> use Bio::Biblio;
> my $biblio = new Bio::Biblio (-access => 'biofetch');
> my $ref = $biblio->get_by_id('15519282');
> 
> I get the error message:
> 
> ------------- EXCEPTION  -------------
> MSG: retrieval type pipeline unsupported
> 
> STACK
> Bio::DB::Biblio::biofetch::get_seq_stream
> /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:237
> STACK
> Bio::DB::DBFetch::get_Stream_by_id
> /opt/csw/share/perl/site_perl/Bio/DB/DBFetch.pm:194
> STACK
> Bio::DB::Biblio::biofetch::get_by_id
> /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:153
> STACK toplevel bbt4.pl:7
> 
> --------------------------------------
> 
> I've tried this on 1.3 (on Solaris) and 1.5.1 (using OS X) and get the
> same error message.
> 
> Can anyone tell me what I'm doing wrong?
> 
> Thanks
> 
> Chihiro