[Bioperl-l] ESummary document

[Chris Fields]

Luis,

You should be able to use the Bio::Tools::EUtilities parsers directly:
  
  # from Bio::DB::EUtilities
  $factory->get_Response(-file=>$file);

  my $parser = Bio::Tools::EUtilities->new(
     -eutil    => 'einfo', 
     -file     => $file);

  while (my $docsum = $parser->next_DocSum) { ... }

There are some small caveats to this, but basically 95% or more of Bio::DB::EUtilities is just glue for submitting queries and passing the response output to the proper Bio::Tools::EUtilities parsers.

chris

On Apr 23, 2011, at 9:39 AM, Luis-Miguel Rodríguez Rojas wrote:

> Hello,
> 
> Does anyone now how can I initialize a
> Bio::Tools::EUtilities::Summary::DocSum object from a DocSum file?
> 
> Say, a script contains the following code:
> 
> my $factory = Bio::DB::EUtilities->new(-eutil => 'esummary', ...);
> $factory->get_Response(-file=>$file);
> 
> Which effectively saves an eSummaryResult XML file in $file.  If I want to
> retrieve the result from within the script, it is easy:
> 
> my $docsum = $factory->next_DocSum;
> 
> But, what about reading the file from another script?  I did not find
> related documentation.
> 
> Thanks, and congrats for the recent release.
> LRR
> 
> --
> Luis M. Rodriguez-R
> [ http://thebio.me/lrr ]
> ---------------------------------
> UMR Résistance des Plantes aux Bioagresseurs - Group effecteur/cible
> Institut de Recherche pour le Développement, Montpellier, France
> [ http://bioinfo-prod.mpl.ird.fr/xantho | Luismiguel.Rodriguez at ird.fr ]
> +33 (0) 6.29.74.55.93
> 
> Unidad de Bioinformática del Laboratorio de Micología y Fitopatología
> Universidad de Los Andes, Bogotá, Colombia
> [ http://lamfu.uniandes.edu.co | luisrodr at uniandes.edu.co ]
> +57 (1) 3.39.49.49 ext 2777
> 
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