IDCONVERT(1)

📦 version 3.0.18342, in debian bookworm, ubuntu jammy, ubuntu noble, ubuntu resolute

💖 IDCONVERT(1) 💖

okay bestie, welcome to the General Commands Manual glow-up edition of idconvert 💅 she's a lil command-line girlie from the libpwiz-tools package and she lives in section 1 of the manual, which is where all the main character executables hang out ✨

🌸 NAME 🌸

idconvert — convert mass spectrometry identification file formats 🧪🦋

🎀 SYNOPSIS 🎀

idconvert [options] [filemasks]

✨ DESCRIPTION ✨

so like, this manual page documents briefly the idconvert software that ships inside the libpwiz-tools package 💖 This program lets you convert mass spectrometry protein identification data files from one format to another. that's it. that's the whole vibe. format in, format out, no cap 🔥

👑 OPTIONS 👑

  • -v | --verbose — spill the tea on everything: displays detailed processing progress information 🫖
  • -f | --filelist filename — uses the contents of filename, which is a file that lists filenames 📝 (a list of lists, very meta of her)
  • -o | --outdir dir — sets the output directory to dir ('-' means stdout btw 💀). default? it's '.', aka the current working directory, aka right where you're standing 🏠
  • -c | --config filename — sets the configuration file to filename ⚙️
  • -e | --ext ext — sets the extension of the output files to ext. can be mzid or pepXML or txt 🏷️
  • --mzIdentML — write mzIdentML format. this is the default, so she's doing it even when you don't ask 👑
  • --pepXML — write pepXML format 🦋
  • --text — write hierarchical text format 📄

🌈 EXAMPLES 🌈

convert sequest.pepXML to sequest.mzid:

idconvert sequest.pepXML

convert mascot.mzid to mascot.pepXML:

idconvert mascot.mzid --pepXML

use a configuration file:

idconvert xtandem.pep.xml -c config.txt

💀 RETURN VALUE 💀

the number of failed files. yes bestie, she's reporting her Ls as a number. that's the exit status, that's how you know 😭

🫶 AUTHOR 🫶

Filippo Rusconi <lopippo@debian.org> — icon, legend, wrote the software and also wrote this manual page 💜

This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation 📜✨

On a Debian system the complete text of the GNU General Public License version 3 can be found in the file /usr/share/common-licenses/GPL-3 — go read it if that's your thing, i respect the hustle 📖💅

and that's the whole page, bestie 🎀 she's IDCONVERT(1) from the libpwiz-tools crew, initial writing dated 05 december 2013, and she ate, periodt 💖🦋⭐

📦 where this page comes from