hmmconvert(1)

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

✨ hmmconvert — NAME ✨

okay so hmmconvert is that girl whose whole job is converting profile files into whatever format you need 💅 it's giving "glow-up but for file formats" fr fr

🦋 SYNOPSIS 🦋

hmmconvert [options] hmmfile

💖 DESCRIPTION 💖

so bestie, the hmmconvert utility takes an input profile file and converts it into different HMMER formats. that's it, that's the whole vibe. iconic behavior honestly 👑

by default? the input profile can be in any HMMER format — and when I say any, I mean it, including the old/obsolete formats from HMMER2, ASCII or binary. no judgment, we love a vintage moment 🎀 the output profile though? that's a current HMMER3 ASCII format. periodt.

oh and hmmfile can be - (dash, yes just a lil dash) which means you're reading this input from stdin instead of from an actual file. shy input energy, we respect it 🙈

🌸 OPTIONS 🌸

  • -h — help! prints a brief lil reminder of the command line usage plus all the available options. a quick lil recap, cute, efficient ✨
  • -a — outputs the profiles in ASCII text format. this is the default, so if you do nothing, you already ate 💅
  • -b — outputs the profiles in binary format. for when you want it inscrutable and compact 🖤
  • -2 — outputs in legacy HMMER2 ASCII text format, in ls (glocal) mode. this is the time-travel option bestie — it lets HMMER3 models get converted back into a close approximation of HMMER2, for comparative studies. not a perfect restoration, an approximation, so keep your expectations realistic 🫶
  • --outfmt <s> — outputs in a HMMER3 ASCII text format other than the most current one. valid choices for <s> are 3/a through 3/f. the current format is 3/f, and that's the default. the format 3/b was used in the official HMMER3 release, and the others were used in the various testing versions. so like, 3/b is the one that actually went out into the world, and the rest are the test-run girlies ⭐

🌈 SEE ALSO 🌈

peep hmmer(1) for a master man page with a whole list of all the individual man pages for programs in the HMMER package — it's the group chat index, iykyk 📚

for the complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page at http://hmmer.org/ 🦋

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

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

🎀 AUTHOR 🎀

http://eddylab.org

and then there's just a lone " sitting there at the end with no partner. mystery quote mark, main character energy, we don't question her 💀

ok that's the whole page bestie, no notes, you're gonna convert those profiles and slay 🔥

and a lil sign-off for the girlies: this is HMMER 3.4, dated Aug 2023, and yes this whole thing is hmmconvert(1) — that's the manual section, not a typo, that's just how man pages count, periodt 💖

📦 where this page comes from