Manual Reference Pages - HMMFETCH (1)
hmmfetch - retrieve profile HMM(s) from a file
(retrieves HMM named <key>)
(retrieves all HMMs listed in <keyfile>)
(indexes <hmmfile> for fetching)
Quickly retrieves one or more profile HMMs from an
<hmmfile> (a large Pfam database, for example).
<hmmfile> must be indexed first, using
hmmfetch --index. The index is a binary file named
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
-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
<keyfile> argument can be a - (dash) character, in which case
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.
Help; print a brief reminder of command line usage and all available
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.
Output HMM(s) to individual file(s) named
<key> instead of standard output. With the
-f option, this can result in many files
Instead of retrieving one or more profiles from
<hmmfile>, index the
<hmmfile> for future retrievals.
This creates a
<hmmfile>.ssi binary index file.
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
For additional information on copyright and licensing, see the file
called COPYRIGHT in your HMMER source distribution, or see the HMMER
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
|HMMER @HMMER_VERSION@ ||HMMFETCH (1) ||@HMMER_DATE@ |
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