Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
hmmfetch(1)			 HMMER Manual			   hmmfetch(1)

NAME
       hmmfetch	- retrieve profiles from a file

SYNOPSIS
       hmmfetch	[options] hmmfile key
	(retrieve HMM named key)

       hmmfetch	-f [options] hmmfile keyfile
	(retrieve all HMMs listed in keyfile)

       hmmfetch	--index	[options] hmmfile
	(index hmmfile for fetching)

DESCRIPTION
       Quickly	retrieves  one	or  more profile HMMs from an hmmfile (a large
       Pfam database, for example).

       For maximum speed, the hmmfile should be	indexed	first, using  hmmfetch
       --index.	  The index is a binary	file named hmmfile.ssi.	 However, this
       is optional, and	retrieval will still work from unindexed files,	albeit
       much more slowly.

       The  default mode is to retrieve	a single profile by name or accession,
       called the key.	For example:

	   % hmmfetch Pfam-A.hmm Caudal_act
	   % hmmfetch Pfam-A.hmm PF00045

       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	delim-
       ited datafiles to be used as a keyfile.

       When using -f and a keyfile, if hmmfile has been	indexed, the keys  are
       retrieved  in the order they occur in the keyfile, but if hmmfile isn't
       indexed,	keys are retrieved in the order	they  occur  in	 the  hmmfile.
       This is a side effect of	an implementation that allows multiple keys to
       be retrieved even if the	hmmfile	is  a  nonrewindable  stream,  like  a
       standard	input pipe.

       In  normal  use	(without  --index  or  -f options), hmmfile may	be '-'
       (dash), which means reading input from stdin rather than	a file.	  With
       the  --index  option, hmmfile may not be	'-'; it	does not make sense to
       index a standard	input stream.  With the	-f option, either  hmmfile  or
       keyfile	(but not both) may be '-'.  It is often	particularly useful to
       read keyfile from standard input, because this allows use to use	 arbi-
       trary  command line invocations to create a list	of HMM names or	acces-
       sions, then fetch them all to a new file, just with one command.

       By default, fetched HMMs	are printed to standard	output in HMMER3  for-
       mat.

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 (an	HMM name or accession).	 Blank lines and  com-
	      ment lines (that start with a # character) are ignored.

       -o _f_ Output HMM(s) to file _f_	instead	of to standard output.

       -O     Output  HMM(s)  to individual file(s) named key instead of stan-
	      dard output.

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

SEE ALSO
       See hmmer(1) for	a master man page with a list of  all  the  individual
       man pages for programs in the HMMER package.

       For  complete documentation, see	the user guide that came with your HM-
       MER distribution	(Userguide.pdf); or see	the HMMER web page (http://hm-
       mer.org/).

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	HMMER source distribution, or  see  the	 HMMER
       web page	(http://hmmer.org/).

AUTHOR
       http://eddylab.org

HMMER 3.3			   Nov 2019			   hmmfetch(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=hmmfetch&sektion=1&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help