NAME

       cmfetch - retrieve covariance model(s) from a file

SYNOPSIS

       cmfetch [options] <cmfile> <key>
        (retrieves CM named <key>)

       cmfetch -f [options] <cmfile> <keyfile>
        (retrieves all CMs listed in <keyfile>)

       cmfetch --index [options] <cmfile>
        (indexes <cmfile> for fetching)

DESCRIPTION

       Retrieves one or more CMs from an <cmfile> (a large Rfam database, for example).

       To enable very fast retrieval, index the <cmfile> first, using cmfetch --index.  The index
       is a binary file named <cmfile>.ssi.

       The default mode is to retrieve a single CM by name or accession, called the  <key>.   For
       example:

         % cmfetch Rfam.cm tRNA
         % cmfetch Rfam.cm RF00005

       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 <cmfile> has been indexed, the keys are retrieved in the
       order  they  occur  in the <keyfile>, but if <cmfile> isn't indexed, keys are retrieved in
       the order they occur in the <cmfile>.  This is a side effect  of  an  implementation  that
       allows  multiple keys to be retrieved even if the <cmfile> is a nonrewindable stream, like
       a standard input pipe.

       In normal use (without --index or -f options), <cmfile> may be  '-'  (dash),  which  means
       reading input from stdin rather than a file.  With the --index option, <cmfile> may not be
       '-'; it does not make sense to index a standard input stream.  With the -f option,  either
       <cmfile>  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 CM names or accessions, then fetch them all to a new file,
       just with one command.

       By default, the CM is printed to standard output in Infernal-1.1 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> (a CM name
              or accession).  Blank lines and comment lines (that start with a #  character)  are
              ignored.

       -o <f> Output CM(s) to file <f> instead of to standard output.

       -O     Output CM(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 <cmfile>, index  the  <cmfile>  for
              future retrievals.  This creates a <cmfile>.ssi binary index file.

SEE ALSO

       See  infernal(1)  for  a  master  man page with a list of all the individual man pages for
       programs in the Infernal package.

       For complete documentation, see the user guide that came with your  Infernal  distribution
       (Userguide.pdf); or see the Infernal 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 Infernal source distribution, or see the Infernal web page ().

AUTHOR

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