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

✨ NAME ✨

Bio::DB::GFF::Aggregator::wormbase_gene — it's the Wormbase gene aggregator bestie, and yes she's doing the most 💅

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🌸 SYNOPSIS 🌸

use Bio::DB::GFF;

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

-------------------------------------------------------------------------------------
Aggregator method: transcript
Main method:       Sequence
Sub methods:       CDS UTR TSS PolyA
-------------------------------------------------------------------------------------

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🦋 DESCRIPTION 🦋

okay so real talk — this aggregator was literally written to be compatible with the C elegans GFF files. No cap.

What does she do? She takes all those raw CDS, 5'UTR, 3'UTR, polyA and TSS features and aggregates them into transcript features. Iconic behavior, honestly. 🎀

And because the Sanger GFF format has ✨idiosyncrasies✨ (iykyk), she expects that the full range of the transcript is contained in a main feature of type Sequence. That's the vibe. That's the whole vibe check.

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💜 method

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

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💜 part_names

• Title — part_names
• Usage — $aggregator->part_names
• Function — return the methods for the sub-parts
• Returns — the list "CDS", "UTR", "TSS", "PolyA"
• Args — none
• Status — Public

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💜 main_name

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

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💀 BUGS 💀

None reported. (we love a clean record, not a single one, she's unproblematic fr fr 🫶)

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👑 SEE ALSO 👑

• 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!! this lil doc came from perl v5.40.0 and was dated 2024-10-20, so go forth and aggregate those transcripts, you absolute main character 🌈⭐💅