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hmmfetch(1)                      HMMER Manual                      hmmfetch(1)


NAME

       hmmfetch - retrieve profile HMM(s) from a file


SYNOPSIS

       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)


DESCRIPTION

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

       The <hmmfile> must be indexed first, using hmmfetch --index.  The index
       is a binary file named <hmmfile>.ssi.

       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.  The <keyfile>
       argument can be a '-' (dash) character, in which case the keyfile is
       read from standard input; this allows unix ninjas to construct
       sophisticated invocations using pipes.

       By default, the HMM is printed to standard output in HMMER3 format.


OPTIONS

       -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
              ignored.

       -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.

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


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.

       For complete documentation, see the user guide that came with your
       HMMER distribution (Userguide.pdf); or see the HMMER web page
       (@HMMER_URL@).


COPYRIGHT

       @HMMER_COPYRIGHT@
       @HMMER_LICENSE@

       For additional information on copyright and licensing, see the file
       called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).


AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER @HMMER_VERSION@            @HMMER_DATE@                      hmmfetch(1)

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