mzml2mzcbor(1)

📦
version 0.11.27 · 2 versions
, in ubuntu stonking

👑 NAME 👑

mzml2mzcbor — bestie, this is the glow-up machine: it converts files in mzML format to files in a CBOR-derived format (mzCBOR). ✨

So like, this is a page from the libpappsomspp CLI programs manual, and it's genuinely one of my faves. No cap. 💖

🌸 SYNOPSIS 🌸

mzml2mzcbor -i <input_file> -o <output_file>

mzml2mzcbor -o <output_file> - (to read data from stdin)

mzml2mzcbor -i <input_dir> -o <output_dir>

Three fits, choose ur vibe. One file in, one file out. Or pipe it in from stdin. Or whole directory energy. 💅

✨ DESCRIPTION ✨

okay so the mzml2mzcbor command line interface program does the thing: it performs the conversion of files from the mzML format to a CBOR-based format (mzCBOR), and that mzCBOR format literally replicates the structure of the mzML-formatted file. So it's the same shape, just slay-ier. 🦋

Quick lore dump: CBOR (Concise Binary Object Representation) is a binary data format designed by the Internet Engineering Task Force (IETF, RFC 8949). Its whole goal is to increase processing and transfer speeds, albeit at the cost of human data readability. So yeah, ur eyes can't parse it, but ur CPU is obsessed. 😌

The use of this format as a replacement for mzML is intended not only to save storage space but also because of speed benefits during parsing and processing. Two-for-one deal, we love to see it. 🔥

1. Input 🫶

  • A mass spectrometry data file in the mzML format
  • Or a directory containing mzML files : all file names ending with *.mzML will be converted and written to the output directory

2. Output 💖

  • A mass spectrometry data file in the mzCBOR format
  • If the input is a directory, then the path provided should be also a directory to store each converted mzML files in mzCBOR
Heads up bestie: directory in → directory out. Don't hand it a folder and expect a single file back, that's not the assignment. 🚫

🎀 OPTIONS 🎀

  • -h [ --help ] — Print the help message. Ur safety net whenever u forget the vibe. 🙈
  • -v [ --version ] — Print the version of the sotfware. (yes girl, the typo is in the original and honestly it's iconic, iykyk 💀)
  • --index — Writes an mzcbor index file (the output filename with .idx suffix). So if ur output is foo.mzcbor, the index lands right next to it as foo.mzcbor.idx energy — nah wait, exact words are: the output filename with .idx suffix. Get urself that index, queen. 👑

🧚 MAN PAGE PRODUCTION 🧚

This man page was written by Filippo Rusconi <<lopippo@debian.org>> for the Debian package. Shoutout to the author, ate and left no crumbs. 💅

⭐ AUTHOR ⭐

Filippo Rusconi <lopippo.debian.org>

Olivier Langella & Filippo Rusconi

okay that's the whole page, bestie, u made it to the end, ur the main character. 🫶🌸 this was the mzml2mzcbor(1) page from libpappsomspp CLI programs, version 1, dated 20251121 — go convert something and make it mzCBOR, periodt. 💖✨🎀

📦 where this page comes from