cmpress(1)

📦
version 1.1.5 · 2 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💅 cmpress — the glow-up your CM database needed

okay so bestie, welcome to cmpress, a page from the Infernal Manual (that's the cmpress(1) manual, section 1, iykyk). she's the one who gets your covariance models ready for their main character moment in cmscan. let's get into it 🫶

✨ NAME ✨

cmpress — prepare a covariance model database for cmscan

like, literally her whole job. no notes. 💖

🦋 SYNOPSIS 🦋

cmpress [options] <cmfile>

short. sweet. iconic. <cmfile> is the star of the show.

🌸 DESCRIPTION 🌸

So here's the tea. You start with a CM database called <cmfile>, and it has to be in standard Infernal-1.1 format. From that, cmpress builds binary compressed datafiles for cmscan. And not to be dramatic but — the cmpress step is required for cmscan to work. like, there is no cmscan without her. periodt.

Also, quick heads up, no skipping steps: <cmfile> must have already been calibrated with cmcalibrate for cmpress to work. she will not run on an uncalibrated model, bestie, that's not a vibe. 😭

Now the fun part — four files get created:

  • <cmfile>.i1m — holds the covariance models, plus their associated filter p7 profile HMMs and all their annotation, in a binary format. the whole squad, boxed up. 📦
  • <cmfile>.i1i — an SSI index for the <cmfile>.i1m file. think of her as the table of contents, she's the finder. 🔍
  • <cmfile>.i1f — precomputed data structures for the fast heuristic filter (the SSV filter) for the filter p7 profile HMMs in <cmfile>. speed. that's the vibe. ⚡
  • <cmfile>.i1p — precomputed data structures for the rest of each profile filter p7 HMM. the leftovers got a home too, no crumbs wasted. 💜
🚫 One lil rule though: <cmfile> may not be '-' (dash). running cmpress on a standard input stream rather than a file is not allowed. she needs a real file, she's not doing the pipe thing, sorry babe. 🙈

🎀 OPTIONS 🎀

  • -h — Help. prints a brief reminder of command line usage and all available options. she'll tell you everything you forgot, no judgment. 💅
  • -F — Force. overwrites any previous cmpress'ed datafiles. the default behavior is to bitch about any existing files and ask you to delete them first — yes that's literally what the man page says, and honestly? valid. she just wants you to be sure before she wrecks your old files. use -F when you're committed. 🔥

👑 SEE ALSO 👑

  • See infernal(1) for a master man page with a list of all the individual man pages for programs in the Infernal package. the whole family tree, all in one place. 🌈
  • For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf); or see the Infernal web page (http://eddylab.org/infernal/). the pdf is thick but she ate. 📖✨

Copyright (C) 2023 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license. slay, free, open, generous. 🫶

For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal source distribution, or see the Infernal web page (http://eddylab.org/infernal/).

⭐ AUTHOR ⭐

http://eddylab.org

🧚 okay that's the whole page bestie, you're officially certified to run cmpress and go live your cmscan dreams. lowkey obsessed with you for reading a man page all the way through, that's main character energy fr fr. 💜

Infernal 1.1.5 — Sep 2023 — cmpress(1) 💅 mwah, bye! 🎀

📦 where this page comes from