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).

       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.

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 ().

COPYRIGHT

       Copyright (C) 2013 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

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

AUTHOR

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

HMMER 3.1b1                                         May 2013                                         hmmfetch(1)