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

💖 Bio::D...script(3pm) — Bio::DB::GFF::Aggregator::processed_transcript 💖

okay bestie, you found the page 💅 this one lives in the User Contributed Perl Documentation corner of the perl universe, and it's literally the manual for Bio::DB::GFF::Aggregator::processed_transcript. pull up a chair, we're doing genomics 🧬✨

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🌸 NAME 🌸

Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology Transcript

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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 => ['processed_transcript'],
                               );

------------------------------------------------------------------------
Aggregator method: processed_transcript
Main method:       mRNA
Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
------------------------------------------------------------------------

like, that little dashed box is the whole personality of this module ngl 🫶

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🦋 DESCRIPTION 🦋

Bio::DB::GFF::Aggregator::processed_transcript is one of the default aggregators, and it was written to be compatible with the Sequence Ontology canonical gene. no cap, that's the whole point of it.

what does it do tho? it aggregates raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and "polyA_site" features into "mRNA" features. it's giving ✨glow-up✨ for your feature table.

and the UTRs? they may also be named "untranslated_region," "five_prime_untranslated_region," "three_prime_untranslated_region,", "5'-UTR," and other synonyms. so many aliases, so little time 😭 it's fine, it handles them.

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🎀 method 🎀

• Title : method
• Usage : $aggregator->method
• Function: return the method for the composite object
• Returns : the string "processed_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 5'-UTR 3'-UTR transcription_start_site polyA_site
• 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 "mRNA"
• Args : none
• Status : Public

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💀 BUGS 💀

None reported.

periodt. not a single one. (don't test it, bestie 🙈)

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🌈 SEE ALSO 🌈

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

go read those next, iykyk 👑

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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 a wrap, babe ✨ this whole lil page was served up by perl v5.30.0 on 2020-01-13, and the manual name stamped on it is Bio::D...script(3pm). mwah, go aggregate something iconic 💖🎀🦋