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

🎀 NAME 🎀

Bio::DB::GFF::Aggregator::gene — it's the Sequence Ontology Geene situation, bestie ✨

(and yes, that's the gene aggregator living inside the Bio::DB::GFF::Aggregator crew, iykyk 💅)

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✨ SYNOPSIS ✨

okay so here's literally how you summon it:

  use Bio::DB::GFF;

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

and here's the whole vibe of what it does, laid out for you 🫶

------------------------------------------------------------------------
Aggregator method: gene
Main method:       mRNA
Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site
------------------------------------------------------------------------

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💖 DESCRIPTION 💖

so Bio::DB::GFF::Aggregator::gene is identical to so_transcript, fr fr — the only glow-up is the name. You reach for this one when you want the aggregated feature to be called "gene" instead of "processed_transcript". Same energy, different label. periodt.

What it does: it scoops up all the raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and "polyA_site" features and aggregates them into "mRNA" features. iconic behavior honestly.

oh and a lil plot twist 🙈 — those UTRs might also be named "untranslated_region," "five_prime_untranslated_region," "three_prime_untranslated_region," "5'-UTR," and other synonyms. So many nicknames, so little time 💀

🌸 method 🌸

Title   : method
Usage   : $aggregator->method
Function: return the method for the composite object
Returns : the string "gene"
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 5'-UTR 3'-UTR transcription_start_site polyA_site
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, we stay unbothered 👑

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🦋 SEE ALSO 🦋

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

go read those too, bestie, they're the rest of the lore 📚

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👑 AUTHOR 👑

Lincoln Stein <lstein@cshl.org>. 🫶

Copyright (c) 2008 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, mwah 💋 — this gem of a doc comes to you as perl v5.30.0, dated 2020-01-13, straight from the Bio::D...::gene(3pm) files. slay, go aggregate something gorgeous 🌈✨