Bio::R...eMatrix(3pm)

💖 NAME 💖

Bio::Roary::PresenceAbsenceMatrix — bestie, it makes a matrix. A presence/absence matrix. That's literally the whole job 🦋

Oh and btw, this page is from the User Contributed Perl Documentation collection, filed under Bio::R...eMatrix(3pm) if you're looking for it in the stacks ✨

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🌸 VERSION 🌸

version 3.13.0 — she's serving, she's current 👑

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✨ SYNOPSIS ✨

okay so here's the tea: you're building a matrix that says who's present and who's absent. And the reason you do it this way is because generating all those inputs is computationally intensive 😭 like, do not do that twice. So the move is: calculate everything once over in the GroupStatistics module, then just pass it all through here. Efficiency queen behavior 💅

use Bio::Roary::PresenceAbsenceMatrix;

my $obj = Bio::Roary::PresenceAbsenceMatrix->new(
  annotate_groups_obj => $annotate_groups_obj,
  output_filename     => 'gene_presence_absence.Rtab',
  sorted_file_names   => $sorted_file_names,
  groups_to_files     => $groups_to_files,
  num_files_in_groups => $num_files_in_groups,
  sample_headers      => $sample_headers,
);
$obj->create_matrix_file;

no cap, that's it. hand her the annotate_groups_obj, tell her where the output_filename goes (spoiler: 'gene_presence_absence.Rtab' in the example, iconic name fr fr), hand over your sorted_file_names, your groups_to_files, your num_files_in_groups and your sample_headers 🌈 then call create_matrix_file and let her cook 🍓

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🎀 AUTHOR 🎀

Andrew J. Page <ap13@sanger.ac.uk> — thank you king, we appreciate you 🫶💜

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💜 COPYRIGHT AND LICENSE 💜

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

And it's free software, bestie! Licensed under:

The GNU General Public License, Version 3, June 2007

So go off, remix, redistribute — just respect the license, periodt 💅✨

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mwah 💋 that's the whole page. she was documented with perl v5.30.0 back on 2019-11-08 — vintage but still eating, love that for her 🦋🌸