hmmfetch(1) HMMER Manual hmmfetch(1)NAMEhmmfetch - retrieve profile HMM(s) from a file
SYNOPSIShmmfetch [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 sophis‐
ticated 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 sin‐
gle <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 stan‐
dard 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 <hmm‐
file>.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)
