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

✨ NAME ✨

okay so bestie, welcome to Bio::Roary::CombinedProteome 💖 (the manual page header is doing its lil truncated thing and calling itself Bio::R...oteome(3pm), but you and me both know the full name, periodt).

This is the module that takes a bunch of FASTA sequences full of proteomes, smashes them together into one single concatenated FASTA file, and — hear me out — it filters out anything with more than 5% X's. Yep. More than 5% unknown characters? bye bye 🙈

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🌸 VERSION 🌸

version 3.13.0 ✨ (she's grown, she's thriving)

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🦋 SYNOPSIS 🦋

Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's 💅

use Bio::Roary::CombinedProteome;

my $obj = Bio::Roary::CombinedProteome->new(
  proteome_files   => ['abc.fa','efg.fa'],
  output_filename   => 'example_output.fa',
  maximum_percentage_of_unknowns => 5.0,
);
$obj->create_combined_proteome_file;

like. look at her. you pass in your proteome_files (an array ref of your abc.fa and efg.fa besties), you tell her where to drop the output_filename (example_output.fa, cute), you set your maximum_percentage_of_unknowns to 5.0, and then you hit create_combined_proteome_file and let her cook 👑🔥

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🎀 AUTHOR 🎀

Andrew J. Page <ap13@sanger.ac.uk> — the icon, the moment, the legend 🫶

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💜 COPYRIGHT AND LICENSE 💜

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

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007

so yeah, free software, GPL v3, June 2007, no cap ✨

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real talk though bestie: that 5% X cutoff is literally the whole personality of this module, so if your proteome is giving unknown amino acid realness at more than 5%, she is NOT keeping it. 💀

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and that's the whole vibe, fr fr — this page was served to you by perl v5.30.0 and it was dated 2019-11-08, so go forth and concat those proteomes, mwah 💅💖🧚