Bio::D...iofetch(3pm)

💖 Bio::DB::Biblio::biofetch — bestie edition 💖

okay so this is the Bio::DB::Biblio::biofetch page from the User Contributed Perl Documentation section of the manual (manpage name Bio::D...iofetch(3pm), in case you were wondering), and it's literally the whole vibe of "get me a citation, but make it BioFetch". 🧚✨

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✨ NAME ✨

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

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🌸 VERSION 🌸

version 1.70 💅

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🦋 SYNOPSIS 🦋

okay so do not use this object directly, bestie. like, only access it through the Bio::Biblio module. that's the rule. 🙈

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";
}

(and yes, that extra ) in the get_by_id line is exactly how it's written here. not me fixing it. it's giving iconic typos only. 💀)

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🌈 DESCRIPTION 🌈

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

The main documentation details are to be found in Bio::DB::BiblioI — go read that one too, it's the main character. 👑

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💜 ATTRIBUTES 💜

🍓 Defaults 🍓

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

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💅 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

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😭 BUGS AND LIMITATIONS 😭

• Only method get_by_id() is supported

fr fr. that's the whole list. one (1) supported method. the way that the others are just... vibes. 🫶

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🎀 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. (they want to hear from you, no cap 💖)

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.

pro tip from the page itself: go to the list, not the maintainer's DMs. and bring receipts (code + data examples). ✨

🐛 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/

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👑 LEGAL 👑

✍️ Authors

Heikki Lehvaslaiho <heikki@bioperl.org>

📜 Copyright and License

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

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okay that's the whole page, bestie, no notes, we ate. 🍓💜

and for the cute sign-off: this gorgeous little document came out of perl v5.36.0, dated 2023-02-14, so happy valentine's day to this manpage specifically, mwah 💅💖✨