hmmconvert(1) [debian man page]

hmmconvert(1)							   HMMER Manual 						     hmmconvert(1)

NAME

       hmmconvert - convert profile file to a HMMER format

SYNOPSIS

       hmmconvert [options] <hmmfile>

DESCRIPTION

       The hmmconvert utility converts an input profile file to different HMMER formats.

       By  default,  the input profile can be in any HMMER format, including old/obsolete formats from HMMER2, ASCII or binary; the output profile
       is a current HMMER3 ASCII format.

OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       -a     Output profiles in ASCII text format. This is the default.

       -b     Output profiles in binary format.

       -2     Output in legacy HMMER2 ASCII text format, in ls (glocal) mode. This allows HMMER3 models to be converted back to a close approxima-
	      tion of HMMER2, for comparative studies.

       --outfmt <s>
	      Output  in a HMMER3 ASCII text format other then the most current one.  Valid choices for <s> are 3/b or 3/a.  The current format is
	      3/b, and this is the default. There is a slightly different format 3/a that was used in some alpha test code.

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  HMMER  distribution  (Userguide.pdf);  or	see  the  HMMER  web  page
       (@HMMER_URL@).

COPYRIGHT

       @HMMER_COPYRIGHT@
       p@HMMER_LICENSE@

       For  additional	information  on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

       "

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 						     hmmconvert(1)

hmmfetch(1)							   HMMER Manual 						       hmmfetch(1)

NAME

       hmmfetch - retrieve profile HMM(s) from a file

SYNOPSIS

       hmmfetch [options] <hmmfile> <key>
	(retrieves HMM named <key>)

       hmmfetch -f [options] <hmmfile> <keyfile>
	(retrieves all HMMs listed in <keyfile>)

       hmmfetch --index [options] <hmmfile>
	(indexes <hmmfile> for fetching)

DESCRIPTION

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

       The <hmmfile> must be indexed first, using hmmfetch --index.  The index is a binary file named <hmmfile>.ssi.

       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  white-
       space  delimited  datafiles  to	be used as <keyfile>s.	The <keyfile> argument can be a '-' (dash) character, in which case the keyfile is
       read from standard input; this allows unix ninjas to construct sophisticated invocations using pipes.

       By default, the HMM is printed to standard output in HMMER3 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> (an HMM name or accession).  Blank lines and comment 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 standard output. With the -f option, this can result in many files being
	      created.

       --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  HMMER distribution (Userguide.pdf); or see the HMMER web page
       (@HMMER_URL@).

COPYRIGHT

       @HMMER_COPYRIGHT@
       @HMMER_LICENSE@

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or  see	the  HMMER
       web page (@HMMER_URL@).

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 						       hmmfetch(1)