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Man Pages


Manual Reference Pages  -  HMMFETCH (1)

NAME

hmmfetch - retrieve profile HMM(s) from a file

CONTENTS

Synopsis
Description
Options
See Also
Copyright
Author

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 whitespace 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

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HMMER @HMMER_VERSION@ HMMFETCH (1) @HMMER_DATE@

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