CHANGE_...NTATION(1p)

📦
version 0.5.4 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

okay bestie, gather round — this page is change_paired_read_orientation, and yeah, the manual name got chopped down to CHANGE_...NTATION(1p) because Unix manpage headers are dramatic like that. What it does is change the orientation of paired-end reads in a FASTA file. That's the whole vibe. ✨

🦋 DESCRIPTION 🦋

So here's the tea: this script takes your paired-end reads and reverses the orientation, meaning it reverse-complements every right-hand paired-end read — those are the ones whose ID ends in /2 — inside a FASTA file. Left reads? Untouched, living their life. Right reads? Flipped and complemented, slay. 💅

🎀 REQUIRED ARGUMENTS 🎀

Not optional, not "maybe later", these two are required fr fr:

  • <in_fasta> — the FASTA file holding the reads you wanna re-orient. Your input, your main character. 🌸
  • <out_fasta> — the output FASTA file where the reads get written. Give it a name, it will not name itself. 💖

Copyright 2009-2012 Florent ANGLY <florent.angly@gmail.com> 🫶

Grinder is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Grinder is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Grinder. If not, see <http://www.gnu.org/licenses/>. 📜

💀 BUGS 💀

Real talk: all complex software has bugs lurking in it, and this program is no exception — it's giving "we're all flawed, it's fine". 🙈 If you find a bug, please report it on the SourceForge Tracker for Grinder:

<http://sourceforge.net/tracker/?group_id=244196&atid=1124737>

Bug reports, suggestions and patches are welcome, periodt. Grinder's code is developed on Sourceforge (<http://sourceforge.net/scm/?type=git&group_id=244196>) and is under Git revision control. To get started with a patch, do:

git clone git://biogrinder.git.sourceforge.net/gitroot/biogrinder/biogrinder

And that's the whole page, bestie!! 🧚 This cutie is from the User Contributed Perl Documentation, running on perl v5.32.0, dated 2020-12-03. Go forth and reverse-complement responsibly. 💜

📦 where this page comes from