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  one  retrieved  HMM  (by  key) to a file named key.  This is a convenience for saving some
              typing: instead of
               % hmmfetch -o RRM_1 hmmfile RRM_1
              you can just type
               % hmmfetch -O hmmfile RRM_1
              The -O option only works if you're retrieving a single profile; it is incompatible with -f.

       --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) 2023 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

HMMER 3.4                                           Aug 2023                                         hmmfetch(1)