cmfetch(1)

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

💖 cmfetch(1) — the Infernal Manual's cutest little retrieval tool 💖

okay bestie, welcome to cmfetch, part of the Infernal manual set. she's the friend who goes into the big giant closet (that's your <cmfile>, think a huge Rfam database) and pulls out exactly the fit you asked for. no digging, no drama. 🎀

✨ NAME ✨

cmfetch — retrieve covariance model(s) from a file 🦋

🌸 SYNOPSIS 🌸

cmfetch [options] <cmfile> <key>
 (retrieves CM named <key>)

cmfetch -f [options] <cmfile> <keyfile>
 (retrieves all CMs listed in <keyfile>)

cmfetch --index [options] <cmfile>
 (indexes <cmfile> for fetching)

💅 DESCRIPTION 💅

So basically, cmfetch retrieves one or more CMs from an <cmfile> — like a big Rfam database, for example. iconic behavior honestly.

To make retrieval very fast (like, speed-of-light fast, no cap), index the <cmfile> first using cmfetch --index. That index? It's a binary file named <cmfile>.ssi. periodt.

The default mode is retrieving a single CM by name or accession, and we call that the <key>. For example:

% cmfetch Rfam.cm tRNA
% cmfetch Rfam.cm RF00005

With the -f option, you hand her a <keyfile> full of one or more keys instead. The first whitespace-delimited field on each non-blank, non-comment line of the <keyfile> gets used as a <key>, and literally any remaining data on that line is just ignored, bye. This means you can use a whole variety of whitespace-delimited datafiles as <keyfile>s. versatility queen 👑

When you're using -f with a <keyfile>, here's the tea: if <cmfile> has been indexed, the keys are retrieved in the order they occur in the <keyfile>, but if <cmfile> isn't indexed, keys are retrieved in the order they occur in the <cmfile>. It's a side effect of an implementation that lets multiple keys be retrieved even when the <cmfile> is a nonrewindable stream — like a standard input pipe. (yes, she said nonrewindable, and yes, that's a real thing 💀)

In normal use (so, without --index or -f options), <cmfile> may be - (dash), which means reading input from stdin instead of a file. With the --index option, <cmfile> may not be -; it genuinely does not make sense to index a standard input stream, bestie, don't try it. With the -f option, either <cmfile> or <keyfile> (but not both) may be -. It is often particularly useful to read <keyfile> from standard input, because this lets you use arbitrary command line invocations to create a list of CM names or accessions, then fetch them all to a new file, all with just one command. one command!! slay. ✨

By default, the CM is printed to standard output in Infernal-1.1 format.

🎀 OPTIONS 🎀

  • -h — Help; print a brief reminder of command line usage and all available options. your girl loves a lil recap. 🫶
  • -f — The second commandline argument is a <keyfile> instead of a single <key>. The first field on each line of the <keyfile> is used as a retrieval <key> (a CM name or accession). Blank lines and comment lines (that start with a # character) are ignored. 🙈
  • -o <f> — Output CM(s) to file <f> instead of to standard output. 📁
  • -O — Output CM(s) to individual file(s) named <key> instead of standard output. one file per key, so organized of her. 💅
  • --index — Instead of retrieving one or more profiles from <cmfile>, index the <cmfile> for future retrievals. This creates a <cmfile>.ssi binary index file. do it once, thank yourself forever. 🔥

🌈 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.

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/). 🦋

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

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

and that's the whole page, bestie!! this one's from Infernal 1.1.5, dated Sep 2023, and it lives at cmfetch(1). go forth and fetch your CMs, you absolute legend 💖✨🌸

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