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hmmfetch - retrieve profile HMM(s) from a file


hmmfetch [options] <hmmfile> <key>
(retrieves HMM named <key>)

hmmfetch -f [options] <hmmfile> <keyfile>
(retrieves all HMMs listed in <keyfile>)

hmmfetch --index [options] <hmmfile>
(indexes <hmmfile> for fetching)


Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam database, for

For maximum speed, the <hmmfile> should be indexed first, using hmmfetch --index. The
index is a binary file named <hmmfile>.ssi. However, this is optional, and retrieval will
still work from unindexed files, albeit much more slowly.

The default mode is to retrieve a single profile by name or accession, called the <key>.
For example:

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

With the -f option, a <keyfile> containing a list of one or more keys is read instead.
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 allows a variety
of whitespace delimited datafiles to be used as <keyfile>s.

When using -f and a <keyfile>, if hmmfile has been indexed, the keys are 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.

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.

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


-h Help; print a brief reminder of command line usage and all available options.

-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

-o <f> Output HMM(s) to file <f> instead of to standard output.

-O Output HMM(s) to individual file(s) named <key> instead of standard output. With
the -f option, this can result in many files being created.

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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