[Bioperl-l] module for pubchem queries

Robert Citek robert.citek at gmail.com
Tue Apr 8 10:09:27 EDT 2008


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


More information about the Bioperl-l mailing list