PSORT(1)

📦 version 3.0.6, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

✨ PSORT(1) — like, the manual for psort bestie ✨

okay so welcome to the psort manual page, you're gonna eat this up 💅

🌸 NAME 🌸

psort — bacterial localization prediction tool 🦠✨

🎀 SYNOPSIS 🎀

psort [-p|-n] [OPTIONS] [SEQFILE]

💖 DESCRIPTION 💖

Runs psort on the sequence file SEQFILE. And if you don't hand it a SEQFILE? No worries bestie, it just reads the sequences from STDIN. lowkey flexible of it 🫶

Here's the whole option menu, no skips, no gatekeeping:

  • --help, -h — shows you the usage info. the "help me I'm lost" button fr fr 🙈
  • --positive, -p — Gram positive bacteria 🦠
  • --negative, -n — Gram negative bacteria 🦠
  • --archaea, -a — Archaea 🧚
  • --cutoff, -c — sets a cutoff value for the reported results ✂️
  • --divergent, -d — sets a cutoff value for the multiple localization flag 🚩
  • --matrix, -m — tells it the path to your pftools installation. if you don't set it, it defaults to whatever the PSORT_PFTOOLS environment variable says 👑
  • --format, -f — picks the sequence format (the default is FASTA) 📄
  • --exact, -e — skips SCLBLASTe. super useful for batch runs of data against itself in SCLBLAST ⚡
  • --output, -o — sets the output format (default is 'normal'). value can be one of: terse, long or normal 🎨
  • --root, -r — specify PSORT_ROOT for running local copies. if you don't set it, it defaults to the value of the PSORT_ROOT environment variable 🏠
  • --server, -s — specifies the PSort server to use ☁️
  • --verbose, -v — be verbose while running, aka spill the tea on everything it's doing 🗣️
  • --x-skip-localization — 💀 (the original page literally gives no description for this one, so that's the whole vibe. it's just there, being mysterious, main character energy)
  • --version — prints the version of PSortb 🔢

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. iconic of him honestly 🫶

and that's the whole page bestie!! this was psort version 3.0.4, dated April 2017 — ty for coming to my ted talk, go localize some bacteria, mwah 💖✨🎀

📦 where this page comes from