Bio::DB::Biblio::biofetch.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::DB::Biblio::biofetch - A BioFetch-based access to a bibliographic
  citation retrieval

SYNOPSIS

Do not use this object directly, only access it through the Bio::Biblio module:
   use Bio::Biblio;
   my $biblio = Bio::Biblio->new(-access => 'biofetch');
   my $ref = $biblio->get_by_id('20063307'));
 
   my $ids = ['20063307', '98276153'];
   my $refio = $biblio->get_all($ids);
   while ($ref = $refio->next_bibref) { 
     print $ref->identifier, "\n";
   }
 
 

DESCRIPTION

This class uses BioFetch protocol based service to retrieve Medline references by their ID.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Heikki Lehvaslaiho (heikki-at-bioperl-dot-org) Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

BUGS AND LIMITATIONS

*
Only method get_by_id() is supported.

APPENDIX

The main documentation details are to be found in Bio::DB::BiblioI.

Here is the rest of the object methods. Internal methods are preceded with an underscore _.

get_by_id

  Title   : get_by_id
  Usage   : $entry = $db->get__by_id('20063307')
  Function: Gets a Bio::Biblio::RefI object by its name
  Returns : a Bio::Biblio::Medline object
  Args    : the id (as a string) of the reference
 
 

get_all

   Title   : get_all
   Usage   : $seq = $db->get_all($ref);
   Function: Retrieves reference objects from the server 'en masse', 
             rather than one  at a time.  For large numbers of sequences, 
             this is far superior than get_by_id().
   Example :
   Returns : a stream of Bio::Biblio::Medline objects
   Args    : $ref : either an array reference, a filename, or a filehandle
             from which to get the list of unique ids/accession numbers.
 
 

get_seq_stream

  Title   : get_seq_stream
  Usage   : my $seqio = $self->get_seq_stream(%qualifiers)
  Function: builds a url and queries a web db
  Returns : a Bio::SeqIO stream capable of producing sequence
  Args    : %qualifiers = a hash qualifiers that the implementing class 
            will process to make a url suitable for web querying
 
 

postprocess_data

  Title   : postprocess_data
  Usage   : $self->postprocess_data ( 'type' => 'string',
                                      'location' => \$datastr);
  Function: process downloaded data before loading into a Bio::SeqIO
  Returns : void
  Args    : hash with two keys - 'type' can be 'string' or 'file'
                               - 'location' either file location or string 
                                            reference containing data
 
 

VERSION and Revision

  Usage   : print $Bio::DB::Biblio::biofetch::VERSION;
            print $Bio::DB::Biblio::biofetch::Revision;
 
 

Defaults

  Usage   : print $Bio::DB::Biblio::biofetch::DEFAULT_SERVICE;