hmmpress(1)

📦
version 3.4 · 2 versions
, in debian trixie, nixos 26.05, nixpkgs unstable, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 hmmpress(1) — the HMMER manual, but make it cute 💖

okay bestie, so this is hmmpress from the HMMER manual, and it's literally the little prep step that makes hmmscan actually work. no cap. let's get into it 🎀

✨ NAME ✨

hmmpress — prep a profile database so that hmmscan can do its thing 💅

🌸 SYNOPSIS 🌸

hmmpress [options] hmmfile

🦋 DESCRIPTION 🦋

So here's the tea: hmmpress builds all the binary compressed datafiles that hmmscan needs, starting from a profile database called hmmfile that's in standard HMMER3 format. And fr fr, this step is required — hmmscan will not work without it. it's giving "prerequisite", it's giving "do this first or perish" 💀

Four files get created, and yes we're listing all of them because each one has main character energy:

  • hmmfile.h3m — holds the profile HMMs and their annotation, all in a binary format 🧚
  • hmmfile.h3i — an SSI index for the hmmfile.h3m file 🔥
  • hmmfile.h3f — precomputed data structures for the fast heuristic filter (that's the MSV filter) ⭐
  • hmmfile.h3p — precomputed data structures for the rest of each profile 👑

And one lil rule you cannot break: hmmfile may not be - (dash). nope nope nope 🙈 running hmmpress on a standard input stream instead of an actual file is not allowed. she needs a real file bestie, she's high maintenance like that.

💖 OPTIONS 💖

  • -h — Help; prints a brief lil reminder of the command line usage and every single option available 🌈
  • -f — Force; overwrites any previous hmmpress'ed datafiles. The default behavior is to bitch about any existing files and ask you to delete them first 😭 (yes, that's really what the man page says, and honestly? iconic)

🫶 SEE ALSO 🫶

  • Check out hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package 📚
  • For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or hit up the HMMER web page at http://hmmer.org/ ✨

Copyright (C) 2023 Howard Hughes Medical Institute. Freely distributed under the BSD open source license. slay, honestly 💚

For additional info on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or check the HMMER web page (http://hmmer.org/) 🎀

🌟 AUTHOR 🌟

http://eddylab.org 🧬

okay that's the whole vibe check, bestie. this was HMMER 3.4, dated Aug 2023, and it's the hmmpress(1) page. go press some profiles, you absolute icon 💅✨🦋

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