Bio::T...oveTags(3pm)

📦
version 1.4.5 · 3 versions
, in debian bookworm, ubuntu jammy

✨ NAME ✨

Bio::Tradis::RemoveTags — bestie, it removes tags from seqs in a fastq file 💅

This is the Bio::T...oveTags page from the 3pm manual (Perl, obviously, she's a Perl module) and she is version 1.4.5 🎀

🌸 VERSION 🌸

version 1.4.5 — yes she's been around a minute, and yes she still slays 🫶

🦋 SYNOPSIS 🦋

okay so here's the whole vibe, no cap:

  • Reads in a fastq file with tradis tags already attached to the start of the sequence 📖
  • Removes tags from the sequence and quality strings ✂️✨
  • Outputs a file *.rmtag.fastq unless an out file is specified 👑
use Bio::Tradis::RemoveTags;

my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc');
$pipeline->remove_tags();

like. that's it. that's the whole thing. iconic behaviour fr fr 💖

🎀 PARAMETERS 🎀

Required 🔥

these ones you cannot skip, they're literally the main character energy of this call:

  • fastqfile — path to/name of file to filter 🗂️ (the one with the tags still stuck on it)
  • tag — the TraDIS tag to remove 🏷️ (this is the tag you want GONE)

Optional ✨

these are the little extras, the accessories to the fit:

  • mismatch — number of mismatches to allow when removing the tag. Default = 0 🙈 (so by default it's a perfect match only, bestie, no wiggle room)
  • outfile — defaults to file.rmtag.fastq for an input file named file.fastq 💾 (she names it for you, very thoughtful of her)

💅 METHODS 💅

  • remove_tags — output all reads with the tags removed to outfile 🎉 literally does what it says on the tin, obsessed

💜 AUTHOR 💜

Carla Cummins <path-help@sanger.ac.uk> 🌸 — thank you for your service, queen 👑

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
quick vibe check: free software, GPL v3, June 2007, 2013 copyright, Wellcome Trust Sanger Institute — that's the whole legal tea, don't @ me ☕💖

and that's the page bestie!! 🥳 this was perl v5.30.0, dated 2020-01-11, from the Bio::T...oveTags(3pm) page — ty for reading, go remove some tags, mwah 💋💅🫶

📦 where this page comes from