.TH "hmmfetch" 1 "@HMMER_DATE@" "HMMER @HMMER_VERSION@" "HMMER Manual"

.SH NAME
hmmfetch - retrieve profile HMM(s) from a file

.SH SYNOPSIS

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

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

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


.SH DESCRIPTION

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

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

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

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

.PP
With the
.I -f
option, a 
.I <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
.I <keyfile> 
is used as a 
.I <key>,
and any remaining data on the line is ignored; this allows
a variety of whitespace delimited datafiles to be used
as 
.I <keyfile>s.
The
.I <keyfile> 
argument can be a '-' (dash) character, in which case
the 
.I keyfile 
is read from standard input; this allows unix ninjas to
construct sophisticated invocations using pipes.

.PP
By default, the HMM is printed to standard output in HMMER3 format.

.SH OPTIONS

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

.TP
.B -f
The second commandline argument is a 
.I <keyfile>
instead of a single 
.I <key>.
The first field on each line of the
.I <keyfile> 
is used as a retrieval 
.I <key>
(an HMM name or accession). 
Blank lines and comment lines (that start with
a # character) are ignored. 

.TP
.BI -o " <f>"
Output HMM(s) to file
.I <f>
instead of to standard output.

.TP
.B -O
Output HMM(s) to individual file(s) named
.I <key>
instead of standard output. With the
.B -f 
option, this can result in many files
being created.

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



.SH SEE ALSO 

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

.PP
For complete documentation, see the user guide that came with your
HMMER distribution (Userguide.pdf); or see the HMMER web page
(@HMMER_URL@).



.SH COPYRIGHT

.nf
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
.fi

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@).


.SH AUTHOR

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