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

💖 NAME 💖

Bio::DB::GFF::Aggregator::match — it's the Match aggregator, bestie ✨ and yes it's coming to you straight from the Bio::D...::match(3pm) manual page, so you know it's the real deal 💅

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🎀 SYNOPSIS 🎀

okay so first things first, you gotta load the thing:

use Bio::DB::GFF;

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

and here's the lil vibe check of what this aggregator is actually doing under the hood:

-------------------------------------------------
Aggregator method: match
Main method:       match
Sub methods:       similarity HSP
-------------------------------------------------

periodt. that's the whole shape of it 🫶

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🌸 DESCRIPTION 🌸

so this aggregator? it's the one for Sequence Ontology-compatible gapped alignments. it's giving organized, honestly.

the way it works is: there's one single top-level alignment called "match", and then a whole lil squad of subalignments hanging off it, called either "similarity" or "HSP". main character + supporting cast energy, we love to see it 👑

also!! go peek at the "alignment" aggregator too, it's literally right there in the family 💜

✨ method ✨

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

like it literally just hands you back "match". no drama, no arguments, iconic behaviour fr fr 💅

🦋 part_names 🦋

• Title : part_names
• Usage : $aggregator->part_names
• Function : return the methods for the sub-parts
• Returns : the list "similarity", "HSP"
• Args : none
• Status : Public

this one gives you the sub-part roster: "similarity" and "HSP". the whole friend group 🫶✨

🌈 main_name 🌈

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

yep, still "match". the main component stays the main component. consistency queen 💖

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💀 BUGS 💀

None reported.

(not me being shocked — zero bugs?? we love a clean record, no cap 🙈✨)

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👀 SEE ALSO 👀

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

go read those too, they're the extended universe 🧚

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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 was perl v5.30.0, dated 2020-01-13, from the Bio::D...::match(3pm) manual — tysm for reading, ily, go write some slay gapped alignments 🌸💖🦋