cmconvert(1)

📦
version 1.1.5 · 3 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💅 cmconvert(1) — the Infernal Manual, bestie edition 🎀

ok so real quick before we dive in: this whole page lives inside the Infernal Manual, and the star of the show is cmconvert. she converts covariance model files. that's the whole personality. let's GO ✨

🦋 NAME

cmconvert — converts Infernal covariance model files, no cap 💖

🌸 SYNOPSIS

cmconvert [options] <cmfile>

✨ DESCRIPTION

okay so the cmconvert utility does exactly what it says on the tin: it converts an input covariance model file to different Infernal formats. literally her only job and she ate 🔥

By default, the input CM file can be any CM file created by Infernal version 1.0 or later, and the output CM file is a current Infernal format. 💫

🚨 heads up bestie: files from versions older than version 1.0 cannot be converted. it's giving "sorry, we don't serve that vintage" 😭

And a cute little trick: <cmfile> may be - (dash), which means reading this input from stdin rather than a file. iconic behaviour honestly 🫶

💅 OPTIONS

  • -h — Help! prints a brief reminder of command line usage and all available options. your little safety net 🧚
  • -a — Output profiles in ASCII text format. this is the default, so if you don't pick anything, this is what you get 💖
  • -b — Output profiles in binary format. compact vibes 🌈
  • -1 — Output in legacy Infernal1 (Infernal v1.0 through v1.0.2) ASCII text format. ⚠️ okay important: due to important changes between version v1.0.2 and v1.1, any E-value statistic parameters calculated by cmcalibrate in <cmfile> will not be written to the converted output file. so like, they just don't make the cut, she said "not coming" 💀
  • --mlhmm — Do NOT output a CM file. Instead, output one maximum likelihood p7 HMM built from each CM in <cmfile> in HMMER3 ASCII text format. the HMM will have been constructed to be as similar as possible to the CM, without modeling secondary structure. this option could be useful for comparative studies of Infernal and HMMER3. cross-domain main character energy 👑
  • --fhmm — Do NOT output a CM file. Instead, output the filter p7 HMM for each CM in <cmfile> in HMMER3 ASCII text format. the filter version specifically, ok? different girl 💜

🔥 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 mothership fr fr 🌟

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/). iykyk 📚

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

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 — that's the whole author line, she's mysterious like that 💫

and that's the tea, bestie 🍓 this page is from Infernal 1.1.5, dated Sep 2023 — go forth and convert your CMs, you absolute icon 💅✨

📦 where this page comes from