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

[t-nakazato at muj.biglobe.ne.jp]

Hi,


If you don't need to use "biofetch" protocol, try "eutils".

use Bio::Biblio;
my $biblio = new Bio::Biblio (-access => 'eutils');  # biofetch -> eutils
my $ref = $biblio->get_by_id('15519282');


And, you can write with perl one liner (on command line).

perl -MBio::Biblio -le 'print Bio::Biblio->new(-access => "eutils")->get_by_id("1551982")'


Takeru



> 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
> 
> -- 
> 
> ----------------------------------------------------------------------
> Chihiro Yamada.
> FlyBase (Cambridge),            http://www.FlyBase.org/
> Department of Genetics,
> University of Cambridge,        email: c.yamada at gen.cam.ac.uk
> Downing Street,                 Tel : 01223-333963
> Cambridge,  CB2 3EH,            FAX : 01223-333992
> United Kingdom.                 Memes don't exist. Spread the Word.
> ----------------------------------------------------------------------
> 
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