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

💖 Bio::DB::GFF::Aggregator::coding 💖

okay bestie, gather round, because today we're talking about Bio::DB::GFF::Aggregator::coding — aka The Coding Region Aggregator — from the User Contributed Perl Documentation. she's a little aggregator module with a big job and honestly? she ate. 🎀

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✨ SYNOPSIS ✨

here's the whole vibe, literally copy-paste energy:

use Bio::DB::GFF;

# Open the sequence database
my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                 -dsn     => 'dbi:mysql:elegans42',
                                 -aggregator => ['coding'],
                               );

and then the little cheat-sheet of what she's working with:

------------------------------------------------------------------------
Aggregator method: coding
Main method:       mRNA
Sub methods:       CDS
------------------------------------------------------------------------

like. main character energy: the aggregator method is coding, the main method is mRNA, and the sub methods are CDS. that's the whole squad. 🫶

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🌸 DESCRIPTION 🌸

so what does she actually do? Bio::DB::GFF::Aggregator::coding aggregates CDS features into a feature called coding, and she was written to be compatible with the Sequence Ontology canonical gene. iconic, honestly. 👑

here's the tea though: the CDS features are expected to belong to a parent of type mRNA — but lowkey the aggregator will still work even if that isn't the case. she's flexible like that. no cap. ✨

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🦋 method 🦋

• Title: method
• Usage: $aggregator->method
• Function: return the method for the composite object
• Returns: the string "coding"
• Args: none
• Status: Public

🦋 part_names 🦋

• Title: part_names
• Usage: $aggregator->part_names
• Function: return the methods for the sub-parts
• Returns: the list (CDS cds)
• Args: none
• Status: Public

🦋 main_name 🦋

• Title: main_name
• Usage: $aggregator->main_name
• Function: return the method for the main component
• Returns: the string "mRNA"
• Args: none
• Status: Public

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💀 BUGS 💀

None reported. not a single one. she's got a clean record fr fr. ✨

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👀 SEE ALSO 👀

go check out her friends, they're all serving:

• Bio::DB::GFF
• Bio::DB::GFF::Aggregator

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🎀 AUTHOR 🎀

Lincoln Stein <lstein@cshl.org>. 💜

Copyright (c) 2001 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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and that's the whole page bestie, mwah 💅 — this one came from the User Contributed Perl Documentation, riding along with perl v5.30.0 and dated 2020-01-13. slay, and good luck out there with your features 🧚🌈⭐