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.

       --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) 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  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