xenial (1) hmmfetch.1.gz

Provided by: hmmer_3.1b2-2_amd64 bug

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 (C) 2015 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