[Bioperl-l] EUtilities term handling

Sendu Bala bix at sendu.me.uk
Thu Oct 5 17:24:34 EDT 2006


Chris Fields wrote:
> 
> I have corrected the EUtilities POD to reflect that all text input needs 
> to be raw as URI encoding is done in the module, which should work (I 
> think).  I plan on committing it tonight.  It also indicates that 
> EUtilities search queries need to be made as if they are regular Entrez 
> queries.  Would that be sufficient?

You may not even need to mention anything about URI encoding, which 
might frighten some people. Something as simple as:

=head1 SYNOPSIS

use Bio::DB::EUtilities;

   my $esearch = Bio::DB::EUtilities->new(-eutil      => 'esearch',
                                          -db         => 'pubmed',
                                          -term       => 'hutP AND xyz',
...

and/or some POD for the new() method:

=head2 new

  Title   : new
...
  Args    : -eutil => ...
            -db    => ...
            -term  => string, an entrez-style query

=cut

would get the point across, I think.

BTW, can the term string be supplied anywhere else other than new()? It 
doesn't matter at all if it can't, I'm just idly wondering if I missed 
anything.


More information about the Bioperl-l mailing list