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Bio::DB::Biblio::biofeUser3Contributed Perl DocumeBio::DB::Biblio::biofetch(3)

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
       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
       ยท
	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;

perl v5.14.1			  2011-07-22	  Bio::DB::Biblio::biofetch(3)
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