[Bioperl-l] Bio::DB:: fails

[Lincoln Stein]

If it isn't too much trouble, could you upgrade to the developer release and 
see if the problem has been improved?  One thing to watch out for, though, is 
that the GenBank module now introduces a 3s delay between requests (at NCBI's 
request), so your test will run a lot slower.  You can pass a -delay=>0 
option when you create the GenBank object if you want to restore no delay, 
but be careful not to do this on large number of accessions.  Use the 
get_Stream_by_accession() method instead.

Lincoln


On Friday 29 November 2002 03:08 pm, michael wrote:
> On Fri, 29 Nov 2002, Lincoln Stein wrote:
> > I have rerun your test, but am unable to reproduce the problem. Please
> > send the exact version of the Bio::DB::GenBank and Bio::DB::EMBL files
> > you are using.  These were changed very extensively last week and I would
> > like to know whether you are using the pre-change or post-change
> > versions.
>
>         Thankyou for looking into this for me...  I'm on a pre-change
> verson,  Should I upgrade to the developer release?
>
>
> # $Id: GenBank.pm,v 1.43 2002/01/19 22:26:18 jason Exp $
> #
> # BioPerl module for Bio::DB::GenBank
>
>
> # $Id: EMBL.pm,v 1.9 2002/02/28 08:26:54 heikki Exp $
> #
> # BioPerl module for Bio::DB::EMBL
> #
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Michael John Lush PhD		 	 Tel:44-20-7679-5027
> Nomenclature Bioinformatics Support 	 Fax:44-20-7387-3496
> HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
> The Galton Laboratory
> University College London, UK
> URL: http://www.gene.ucl.ac.uk/nomenclature/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-- 
Lincoln Stein
lstein@cshl.org