PREDICTNLS(1)

📦
version 1.0.20 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

✨ predictnls — the manual, but make it cute ✨

okay bestie, sit down, hydrate, because we're about to talk about predictnls(1) — a User Commands page that's lowkey a whole bop. it's giving "bioinformatics but make it fashion." let's get into it 💅

🌸 NAME 🌸

predictnls — prediction and analysis of nuclear localization signals. yes, that kind of NLS. no cap. 🧬

🦋 SYNOPSIS 🦋

predictnls [OPTION]

that's it. that's the whole vibe check. one binary, a bunch of options, infinite possibilities. ✨

💖 DESCRIPTION 💖

predictnls is a method for the prediction and analysis of nuclear localization signals (NLS). fr fr, that's literally what it does. it looks at your sequence and goes "hmm, is this protein getting into the nucleus or not, bestie?" 👑

📝 Output format 📝

Self-annotating, bestie. the output explains itself, no detective work required. there are example outputs waiting for you in /usr/share/doc/predictnls/examples — go look, they're iconic. 🌈

📚 REFERENCES 📚

Cokol, M., Nair, R., and Rost, B. (2000). Finding nuclear localization signals. EMBO Rep, 1(5), 411-5.

(the receipts. cite them. academic integrity is main character energy.) 🎀

⭐ OPTIONS ⭐

okay here's the part everyone scrolls to. every single one, no skipping, we don't do that here:

  • debug=[0|1] — debug mode, on or off. it's right there in the name, iykyk.
  • fileIn=<FILE> — your input file, in fasta format. Required. and heads up: only one sequence per file, so don't go trying to sneak a whole genome in there. 🙈
  • fileOut=<FILE> — where the output goes. Required. no output file, no output. simple math.
  • help — help. it helps. 💁
  • html=[0|1|2] — output format, choose your fighter: 0 - text; 1 - html; 2 - both. Default: 0.

and if you ask for both outputs? the text file is named according to the value of fileOut, and the html file gets an .html extension slapped on it. cute, right? 🎀

  • fileSummary=<FILE> — if set, 1 is written into this file if an NLS is found, 0 otherwise. Optional. a little yes/no receipt, we love a binary king. 👑
  • nlsdat=<FILE> — raw nls data, optional. raw. unfiltered. no notes.
  • version — Print version. because sometimes you just gotta know. ⭐

🔥 EXAMPLES 🔥

here's the moment you've been waiting for, the copy-paste:

"predictnls fileIn=/usr/share/doc/predictnls/examples/O49931.fa
fileOut=/tmp/O49931.nls"

ate. no crumbs. 🍓

🌈 ENVIRONMENT 🌈

  • PREDICTNLSCONF — Location of predictnlsrc configuration file to use, overriding other configuration files. it's the "i said what i said" of config files, bestie. 💜

🧚 FILES 🧚

here's the whole config-file hierarchy, from least to most bossy:

  • /usr/share/predictnls/predictnlsrc.default — Default configuration file. See this file for a description of the parameters. (yes, the docs live in the file. go read it, it's right there.) 📖
  • /etc/predictnlsrc — System configuration file, overriding values in /usr/share/predictnls/predictnlsrc.default. it's climbing the ladder. 🪜
  • ~/.predictnlsrc — User configuration file, overriding values in /etc/predictnlsrc. personal. bespoke. yours. 💅
  • $PREDICTNLSCONF — if this environment variable is set, ~/.predictnlsrc is disregarded and the value of the variable is read for configuration options, overriding /etc/predictnlsrc. this one doesn't ask, it just takes over. periodt. 👑

💜 AUTHOR 💜

R. Nair

(C) Copyright 2010, R. Nair License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

bestie, read that last part again. There is NO WARRANTY. so like, it's free, it's yours, go wild, but it is not your safety net. 😭

and that's the whole page! this was predictnls, version 1.0.20, dated 2022-01-18, straight from the User Commands corner of your friendly neighborhood man pages. go predict some nuclear localization signals, you absolute icon. mwah. 💖✨🦋

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