[Bioperl-l] Fetching > 500 sequences

Lincoln Stein lstein at cshl.edu
Fri Mar 26 19:41:29 EST 2004

There may be a bug in Bio::DB::GenBank, or Entrez may have changed its 
behavior again very slightly.  The interface between the two has always been 
quite fragile.  At some point I will work on this again and try to get it 
working, but first.... Have you tried the bioperl-live CVS version?


On Friday 26 March 2004 07:18 pm, Paulo Almeida wrote:
> This is not Bioperl at all, but if you can't solve the problem and you
> really need all the sequences, you can try the WWW::Mechanize module. It
> allows you to submit forms and follow web links through Perl scripts,
> which means you should be able to submit the query and retrieve the
> results by following the "next page" link on each results page.You would
> have to develop your own way of parsing the results pages, so you
> probably don't want to try this method unless you fail to do it with
> Bioperl...
> -Paulo Almeida
> henrik nilsson wrote:
> >Hi,
> >	Thank you very much for your help.  I went through and took out any
> >references to "retmax" in both Bio::DB::Query::GenBank and
> > Bio::DB::GenBank and Bio::DB::NCBIHelper.  Our script first sends a query
> > through
> >Bio::DB::Query::GenBank and that works fine (it only returns the count
> > found, and that count is > 7000).  However, we then actually query
> > GenBank with Bio::DB::GenBank and it only returns 500 despite the fact it
> > should be returning 7000+ (and we really want them all).  I compared both
> > of the scripts which look very similar in what was passed to GenBank.
> >
> >	I was wondering if any other variables would cause the Entrez scripts to
> > only return 500?  We do use mindate/maxdate and we fetch by query string
> > (if that matters).  Any other ideas?
> >
> >Thanks again for all of your help.
> >
> >Rolf
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Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)

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