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