Provided by: infernal_1.1.2-2_amd64 bug


       cmfetch - retrieve covariance model(s) from a file


       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)


       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

         % cmfetch tRNA
         % cmfetch 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.


       -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

       -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.

              Instead of retrieving one or more profiles from <cmfile>, index  the  <cmfile>  for
              future retrievals.  This creates a <cmfile>.ssi binary index file.


       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 (C) 2016 Howard Hughes Medical Institute.
       Freely distributed under a 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 ().


       The Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA