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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 bibliographiccitation 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:https://redmine.open-bio.org/projects/bioperl/
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¶
- •
- 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;
2012-03-02 | perl v5.14.2 |