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Bio::DB::Biblio::biofetch(3pm) User Contributed Perl Documentation Bio::DB::Biblio::biofetch(3pm)

NAME

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

VERSION

version 1.70

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.

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

ATTRIBUTES

Defaults

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

METHODS

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

BUGS AND LIMITATIONS

* Only method get_by_id() is supported

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:

  https://redmine.open-bio.org/projects/bioperl/

LEGAL

Authors

Heikki Lehvaslaiho <heikki@bioperl.org>

This software is Copyright (c) by 2002 European Bioinformatics Institute and released under the license of the same terms as the perl 5 programming language system itself

2023-02-14 perl v5.36.0