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

💖 Bio::DB::GFF::Aggregator::clone — Clone aggregator 💖

okay bestie, you found the page for Bio::DB::GFF::Aggregator::clone, which ships in the Perl manual as Bio::D...::clone(3pm). it's a default aggregator and it's here to glow up your GFF data, no cap. let's get into it 🫶

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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 => ['transcript','clone'],
                               );

and here's the lil cheat-sheet of how it's wired up, literally:

----------------------------------------------------------------------------
Aggregator method: clone
Main method:       -none-
Sub methods:       Clone_left_end Clone_right_end region:Genomic_canonical
----------------------------------------------------------------------------

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🌸 DESCRIPTION 🌸

so Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and it was written to be compatible with the C elegans GFF files. it aggregates raw "Clone_left_end", "Clone_right_end", and "region:Genomic_canonical" features into composite features of type "clone". it's giving ✨data wrangling✨ and it ate 💅

🎀 aggregate 🎀

Title   : aggregate
Usage   : $features = $a->aggregate($features,$factory)
Function: aggregate a feature list into composite features
Returns : an array reference containing modified features
Args    : see L<Bio::DB::GFF::Aggregator>
Status  : Public

the WormBase GFF model is unusual in that clones aren't identified as a single feature with start and stop positions, but as two features: a "left end" and a "right end". and listen — one or both of these features may be absent. 😭 to accommodate this, the aggregator will return undef for the start and/or stop if one or both of the ends are missing. fr fr, it just shrugs and hands you undef, that's the vibe.

🦋 method 🦋

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

🌈 part_names 🌈

Title   : part_names
Usage   : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
Args    : none
Status  : Public

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💀 BUGS 💀

None reported. (iconic behaviour honestly, we love a clean record ✨)

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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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k that's the whole page bestie, go aggregate something gorgeous 💖 this one's from perl v5.30.0, dated 2020-01-13, and it lives in the manual as Bio::D...::clone(3pm). mwah 🎀🫶✨