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

💖 Bio::DB::GFF::Aggregator::so_transcript — Sequence Ontology Transcript 💖

okay bestie, welcome to the manual page for Bio::DB::GFF::Aggregator::so_transcript, which lives in the User Contributed Perl Documentation corner of the world and is giving very "i am a thin wrapper and i know it" energy. let's get into it 🫶

---

✨ NAME ✨

Bio::DB::GFF::Aggregator::so_transcript — Sequence Ontology Transcript. that's it, that's the whole name, no notes 💅

---

🌈 SYNOPSIS 🌈

here's the vibe, in code:

  use Bio::DB::GFF;

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

so like, that little box? that's the summary card. aggregator method is processed_transcript, main method is mRNA, and the sub methods are CDS, exon, five_prime_UTR, three_prime_UTR, transcription_start_site, polyA_site, 5'-UTR, and 3'-UTR. iconic little lineup honestly 🎀

---

🦋 DESCRIPTION 🦋

okay so Bio::DB::GFF::Aggregator::so_transcript</p> is identical to the processed_transcript aggregator — like, same face, same energy, zero difference. and processed_transcript was designed to be compatible with the Sequence Ontology canonical gene. ✨

what it does: it aggregates raw exon, CDS, five_prime_UTR, three_prime_UTR, transcription_start_site and polyA_site features into mRNA features. slay. and the UTRs may also be named untranslated_region, five_prime_untranslated_region, three_prime_untranslated_region, 5'-UTR, and other synonyms — because of course they can, naming things is chaos, we love that for us 😭

big note bestie: the processed_transcript aggregator is loaded by default. so this one is only needed for backward compatibility. fr fr, you probably don't need to summon it yourself, but it's here if you do 💜

---

🧚 method

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

one job, and it does it: hands you back the string "processed_transcript". no args, no drama. 👑

---

🍓 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

it returns the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site — the sub-parts, the little guys, the supporting cast. again: no args. 💅

---

🌸 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

and this one is the main character's name tag — it returns the string "mRNA". main character energy, literally. ✨

---

💀 BUGS 💀

None reported. not a single one. flawless behaviour, allegedly, we're not gonna question it 🙈

---

👑 SEE ALSO 👑

go read these next, bestie:

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

---

💖 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.

---

and that's the whole page!! this one came from the User Contributed Perl Documentation, perl v5.30.0, dated 2020-01-13. go forth and aggregate responsibly, bestie 🫶✨