hmmfetch(1)

💖 NAME 💖

hmmfetch — bestie, this is how you retrieve profiles from a file ✨

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🌸 SYNOPSIS 🌸

Okay so the manual you're holding is hmmfetch(1) from the HMMER manual, and here's the three ways you can call her:

hmmfetch [options] hmmfile key
 (retrieve HMM named key)

hmmfetch -f [options] hmmfile keyfile
 (retrieve all HMMs listed in keyfile)

hmmfetch --index [options] hmmfile
 (index hmmfile for fetching)

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🦋 DESCRIPTION 🦋

So like, the whole point of hmmfetch is quickly grabbing one or more profile HMMs out of an hmmfile — think a big ol' Pfam database, the kind of file that's giving "I contain multitudes" 💅.

For maximum speed, you should index the hmmfile first, with hmmfetch --index. That index is a binary file named hmmfile.ssi. But — and this is important — indexing is optional, and retrieval will still totally work from unindexed files, just much more slowly. No cap.

The default mode is retrieving a single profile by name or accession, and that thing is called the key. For example:

% hmmfetch Pfam-A.hmm Caudal_act
% hmmfetch Pfam-A.hmm PF00045

With the -f option, instead of one key you read a keyfile containing a list of one or more keys. The first whitespace-delimited field on each non-blank non-comment line of the keyfile is used as a key, and any remaining data on the line is ignored. This is so slay because it means a whole variety of whitespace delimited datafiles can be used as a keyfile 🎀.

When you're using -f and a keyfile: if hmmfile has been indexed, the keys get retrieved in the order they occur in the keyfile, but if hmmfile isn't indexed, keys are retrieved in the order they occur in the hmmfile. This is a side effect of an implementation that allows multiple keys to be retrieved even if the hmmfile is a nonrewindable stream, like a standard input pipe. She's doing her best okay 😭

In normal use (without --index or -f options), hmmfile may be - (dash), which means reading input from stdin rather than a file. With the --index option, hmmfile may not be -; it does not make sense to index a standard input stream. With the -f option, either hmmfile or keyfile (but not both) may be -. It is often particularly useful to read keyfile from standard input, because this allows use to use arbitrary command line invocations to create a list of HMM names or accessions, then fetch them all to a new file, just with one command. Obsessed honestly 🫶

By default, fetched HMMs are printed to standard output in HMMER3 format. ✨

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✨ OPTIONS ✨

• -h — Help; print a brief reminder of command line usage and all available options. The "bestie what do I type" button 💖
• -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 (an HMM name or accession). Blank lines and comment lines (that start with a # character) are ignored.
• -o <f> — Output HMM(s) to file <f> instead of to standard output.
• -O — Output one retrieved HMM (by key) to a file named key. This is a convenience for saving some typing: instead of

% hmmfetch -o RRM_1 hmmfile RRM_1

you can just type

% hmmfetch -O hmmfile RRM_1

The -O option only works if you're retrieving a single profile; it is incompatible with -f. 🚫

• --index — Instead of retrieving one or more profiles from hmmfile, index the hmmfile for future retrievals. This creates a hmmfile.ssi binary index file.

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🌈 SEE ALSO 🌈

See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. It's giving ✨table of contents✨.

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

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👑 COPYRIGHT 👑

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 HMMER source distribution, or see the HMMER web page (http://hmmer.org/).

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💜 AUTHOR 💜

http://eddylab.org

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okay that's the whole page bestie, you ate 💅✨ this was hmmfetch(1) from HMMER 3.4, dated Aug 2023 — go forth and fetch those profiles, main character energy only, periodt 🎀🦋