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) 2020 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