[Bioperl-l] Limit on number of Bio::Seqs returned from Bio::DB::GenBank::get_Stream_by_batch

[Lincoln Stein]

Genbank/Entrez has a habit of imposing arbitrary limits on downloads, 
complicating Bio::DB::GenBank and brethren considerably.  

This is not an approved, bioperl-compliant, or even supported solution, but 
as a temporary measure you can use the Boulder::Genbank modules 
(http://stein.cshl.org/software/boulder/) to get the genbank entries you need 
if you don't want to download the entire genbank distribution.  This module 
jumps through several hoops in order to reissue requests when Entrez cuts you 
off.  You can then feed the genbank flat files that Boulder returns to 
Bio::SeqIO to get proper bioperl objects.

Lincoln

On Thursday 25 April 2002 17:05, Ewan Birney wrote:
> On Thu, 25 Apr 2002 CHALFANT_CHRIS_M@Lilly.com wrote:
> > Is there an upper limit on the number of sequences returned by
> > Bio::DB::GenBank::get_Stream_by_batch?  I seem to be limited to 20.  Is
> > there a way to increase this limit?
>
> It is probab;y best to download all teh data locally and use soemthing
> like Bio::Index::GenBank.
>
> > Chris
> > _______________________________________________
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> > Bioperl-l@bioperl.org
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>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
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