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hmmfetch(1) [debian man page]

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)

Check Out this Related Man Page

hmmpress(1)							   HMMER Manual 						       hmmpress(1)

NAME

       hmmpress - prepare an HMM database for hmmscan

SYNOPSIS

       hmmpress [options] <hmmfile>

DESCRIPTION

       Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary compressed datafiles for hmmscan.  The hmmpress step
       is required for hmmscan to work.

       Four files are created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f, and <hmmfile>.h3p.	The <hmmfile>.h3m file contains the  profile  HMMs
       and  their  annotation in a binary format.  The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file.  The <hmmfile>.h3f file con-
       tains precomputed data structures for the fast heuristic filter (the MSV filter).  The <hmmfile>.h3p file contains precomputed data  struc-
       tures for the rest of each profile.

OPTIONS

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

       -f     Force;  overwrites  any  previous hmmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them
	      first.

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@ 						       hmmpress(1)
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