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 (http://eddylab.org/infernal/).

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  Infernal
       source distribution, or see the Infernal web page (http://eddylab.org/infernal/).

AUTHOR

       http://eddylab.org

Infernal 1.1.5                                      Sep 2023                                          cmfetch(1)