Bio::T...Summary(3pm)

💖 NAME 💖

Bio::Tools::EUtilities::Summary — bestie, this is the class that handles data output (XML) from esummary. That's the whole job. She's the summary girlie. 🎀

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✨ VERSION ✨

version 1.77 — that's the one, no cap.

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🌸 SYNOPSIS 🌸

okay so real talk, do NOT go making an instance of this directly, Bio::Tools::EUtilities is the one that does that for you. Look:

#### should not create instance directly; Bio::Tools::EUtilities does this ####

my $esum = Bio::Tools::EUtilities->new(-eutil => 'esummary',
                                       -file => 'summary.xml');
# can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles)

while (my $docsum = $esum->next_DocSum) {
    my $id = $docsum->get_ids;  # EUtilDataI compliant method, returns docsum ID
    my @names = $docsum->get_item_names;
}

also you can use -response (that's for HTTP::Response objects, iykyk) or -fh (that's for filehandles) 💅

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🦋 DESCRIPTION 🦋

This class handles data output (XML) from esummary. Simple as that. 💖

esummary retrieves information in the form of document summaries (docsums) when you pass it a list of primary IDs, or if you're using a previous search history. She's flexible like that. ✨

This module breaks down the returned data from esummary into individual document summaries per ID (using a DocSum object). And because the data in a docsum can be nested (it's giving layers, it's giving onion 🧅), subclasses of DocSums — Item, ListItem, Structure — are also present. So iconic of them honestly.

Further documentation for Link and Field subclass methods is included below. 👑

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🎀 to_string 🎀

• Title — to_string
• Usage — $foo->to_string()
• Function — converts current object to string
• Returns — none
• Args — (optional) simple data for text formatting
• Note — Used generally for debugging and for the print_* methods

lowkey just your classic "turn the object into a string" moment, mostly for debugging and the print_* methods. 🫶

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💌 FEEDBACK 💌

🌈 Mailing lists 🌈

User feedback is an integral part of the evolution of this and other Bioperl modules. Like, genuinely — your comments and suggestions matter SO much. Send them preferably to the Bioperl mailing list, and your participation is much appreciated. fr fr. 🥹

bioperl-l@bioperl.org               - General discussion
https://bioperl.org/Support.html    - 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. Not being shady, it's just that many experienced and reponsive experts will be able look at the problem and quickly address it. (yes bestie, "reponsive" — that's what the original says, we don't fix, we report 📝). Please include a thorough description of the problem with code and data examples if at all possible. The more deets the better. 💅

🐛 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://github.com/bioperl/bio-eutilities/issues

go off, tell them everything. ✨

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👑 AUTHOR 👑

Chris Fields <cjfields@bioperl.org> — the legend, the moment, the main character. 🫡

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⭐ COPYRIGHT ⭐

This software is copyright (c) 2006-2013 by Chris Fields.

This software is available under the same terms as the perl 5 programming language system itself.

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and that's the whole page bestie 💖 — she was written for perl v5.40.0, dated 2025-01-27, and lives in the User Contributed Perl Documentation corner of the manual. slay, bye 🎀✨🦋