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

💖 NAME 💖

Bio::DB::GFF::Aggregator::waba_alignment — bestie, it's a WABA alignment 🧬✨

(also hi yes, the page header up top just says Bio::D...gnment(3pm) and it's from the User Contributed Perl Documentation, in case you were wondering who published this little icon)

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✨ SYNOPSIS ✨

okay so first you gotta actually pull the thing in:

  use Bio::DB::GFF;

  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['waba_alignment'],
                                 );
  # fetch the synthetic feature type "waba_alignment"
  my @waba    = $db->features('waba_alignment');

and then the whole vibe of it is, like, this little summary card:

-------------------------------------------------------------------------------------
Aggregator method: waba_alignment
Main method:       -none
Sub methods:       nucleotide_match:waba_weak nucleotide_match:waba_strong
                   nucleotide_match::waba_coding
-------------------------------------------------------------------------------------

and yes bestie, that double colon in nucleotide_match::waba_coding is literally what it says up there — I am not editing one single character, that's not my job 💅

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🦋 DESCRIPTION 🦋

Bio::DB::GFF::Aggregator::waba_alignment handles the kind of alignments that come out of Jim Kent's WABA program, and it was written to play nice with the C elegans GFF files 🪱💚

what does "aggregates" mean tho? it means it scoops up these feature types:

• nucleotide_match:waba_weak
• nucleotide_match:waba_strong
• nucleotide_match:waba_coding

...and squishes them together into one aggregate type called waba_alignment. slay, honestly ✨

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🎀 method

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

she returns the method for the composite object, and what she hands back is the string "waba_alignment" 🫶

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🌸 part_names

 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list "nucleotide_match:waba_weak", "nucleotide_match:waba_strong" and "nucleotide_match:waba_coding"
 Args    : none
 Status  : Public

this one's the sub-parts plug — it returns the list "nucleotide_match:waba_weak", "nucleotide_match:waba_strong" and "nucleotide_match:waba_coding" 🌈

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💀 BUGS 💀

None reported.

literally nothing, she's unproblematic, no drama, we love a clean record 🙈✨

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👑 SEE ALSO 👑

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

go read those too, bestie, iykyk 📚🦋

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🌈 AUTHOR 🌈

Lincoln Stein <lstein@cshl.org> — author icon, no cap 👑

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.

fr fr that's the license, go forth and redistribute responsibly 💜

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okay that's the whole page!! it's perl v5.40.0, dated 2024-10-20, and this was Bio::D...gnment(3pm) from the User Contributed Perl Documentation 🫶 bye bestie, go align something iconic 💅🎀