NAME

       hmmfetch - retrieve profiles from a file

SYNOPSIS

       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)

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 a keyfile.

       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.

       --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 (http://hmmer.org/).

COPYRIGHT

       Copyright (C) 2019 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/).

AUTHOR

       http://eddylab.org