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

[Chihiro Yamada]

On Wed, 2005-11-02 at 04:42 -0500, Brian Osborne wrote:
> Chihiro,
> 
> What happens when you set the access mode to "soap" or "eutils" rather than
> to "biofetch"?

and

On Wed, 2005-11-02 at 18:54 +0900, t-nakazato at muj.biglobe.ne.jp wrote:
> 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');
> 
> 
-- 
Thanks guys,

Ah, so I guess, soap and eutils are newer modules. I can get them to
work on my mac (Bioperl 1.5.1) But not on the Sun Boxes running 1.3.
(Which I don't have root access to)

I'll hassle my sysadmin to install a newer version.  From the doc it
looks like we'll need 1.5 - is that right?

Incidentally, is either method (soap or eutils) 'better' than the other?

Cheers,

Chihiro

P.S. nice to hear from you Brian!
c;y

--------------------------------------


> 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
> 
> 
-- 

----------------------------------------------------------------------
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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