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cmfetch(1)			Infernal Manual			    cmfetch(1)

       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

       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 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 re-
       maining	data  on  the line is ignored. This allows a variety of	white-
       space 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  <cm-
       file>.  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 ac-
       cessions, 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  for-

       -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 sin-
	      gle  _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 stan-
	      dard output.

	      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 In-
       fernal distribution (Userguide.pdf); or see the Infernal	web page ().

       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 In-
       fernal web page ().

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

Infernal 1.1.3			   Nov 2019			    cmfetch(1)


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