[Bioperl-l] Fetching > 500 sequences

Paulo Almeida paulo.david at netvisao.pt
Fri Mar 26 19:18:01 EST 2004

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 

-Paulo Almeida

henrik nilsson wrote:

>	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.

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