[Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error

Scott Cain scott at scottcain.net
Wed Nov 3 10:59:12 EDT 2010

Hi Gabriel,

It looks to me like you've got a few things going wrong.  First, you
are using single quotes for the right hand side of the -term value.
In perl, single quotes are non-interpolating, which means variables
won't be substituted in.  However, if you switch to double quotes,
you'll still have a problem, because this:


looks like you are trying to access an element of an array called
genename with a constant called SYMB, which of course you aren't, so
the perl interpreter will die with that.  You can rewrite that section
like this:

  $genename . '[SYMB] AND homo_sapiens[ORGN]'

so that the variable interpolation is moved out of the single quotes.


On Wed, Nov 3, 2010 at 7:53 AM, gabriel teku <gabbyteku at gmail.com> wrote:
> I can't get my esearch to work. It's as follows:
> my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
>                                                  -email      => '
> myemail at gmail.com',
>                                                  -term       =>
> '$genename[SYMB] AND homo_sapiens[ORGN]',
>                                                  -db         => 'geo',
>                                                  -usehistory => 'y'
>                                              );
> When I run this using a gene symbol, it works fine.
> But then when I run it as it is with a gene's symbol changed to
> $genename(stores the gene's symbol/name), it fails.
> How can this be fixed?
> Thanks
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

More information about the Bioperl-l mailing list