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

✨ NAME ✨

Bio::DB::GFF::Aggregator::transcript — the Transcript aggregator, bestie 💖

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🌸 SYNOPSIS 🌸

okay so first you pull in the goods:

use Bio::DB::GFF;

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

-------------------------------------------------
Aggregator method: transcript
Main method:       transcript
Sub methods:       exon CDS 5'UTR 3'UTR TSS PolyA
-------------------------------------------------

like… that little boxed summary? it's giving cheat sheet and I'm obsessed 🎀

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🦋 DESCRIPTION 🦋

Bio::DB::GFF::Aggregator::transcript is one of the default aggregators, no cap — it was literally written to play nice with the C elegans GFF files. What does it do? It scoops up all the raw "exon", "CDS", "5'UTR", "3'UTR", "polyA" and "TSS" features and aggregates them into "transcript" features. slay. ✨

But here's the tea: because the Sanger GFF format has idiosyncrasies (their words, not mine, and honestly relatable), it expects the full range of the transcript to live inside a main feature of type "Transcript" — and yes bestie, notice the capital "T" 👑

Internally this module is super simple. like, embarrassingly simple. If you wanna override it with one that recognizes a main feature named "gene", just follow this template fr fr:

my $db = Bio::DB::GFF->new(...etc...)
my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript',
                                               -main_method => 'gene',
                                               -sub_parts => ['exon','CDS']);
$db->add_aggregator($aggregator);

💅 method

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

🧚 part_names

• Title — part_names
• Usage — $aggregator->part_names
• Function — return the methods for the sub-parts
• Returns — the list "intron", "exon" and "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 "transcript"
• Args — none
• Status — Public

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💀 BUGS 💀

None reported. not a single one. the vibes are immaculate, we're thriving 🫶

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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 is Bio::D...script(3pm) from the User Contributed Perl Documentation, straight outta perl v5.30.0, dated 2020-01-13. go forth and aggregate, periodt 💅