[Bioperl-l] module for pubchem queries

Chris Fields cjfields at uiuc.edu
Tue Apr 8 11:10:26 EDT 2008


Just to note, the the API has changed significantly from the interface  
in the 1.5.2 release.  The up-to-date (supported) interface is in  
subversion; there are some example recipes here:

http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

I'm working on a full HOWTO, just haven't had time to get it up on the  
wiki yet.

chris

On Apr 8, 2008, at 9:09 AM, Robert Citek wrote:

> Wrapping bioperl around eutils will work just fine.  Thanks for the  
> pointer.
>
> http://search.cpan.org/~sendu/bioperl-1.5.2_102/Bio/DB/EUtilities.pm
>
> Regards,
> - Robert
>
> On Fri, Apr 4, 2008 at 4:25 PM, Chris Fields <cjfields at uiuc.edu>  
> wrote:
>> Do you need something to access eutils via BioPerl, or are you  
>> looking for a
>> specific set of classes?  I wrote an interface to eutils
>> (Bio::DB::EUtilities), you could do something like this:
>>
>> #!/usr/bin/perl -w
>>
>> use strict;
>> use warnings;
>> use Bio::DB::EUtilities;
>>
>> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>>                                     -term => 'dihydroorotate',
>>                                     -db => 'pcsubstance',
>>                                     -retmax => 1000);
>>
>> print join(',',$eutil->get_ids)."\n";
>>
>> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list