hmmfetch(1) | HMMER Manual | hmmfetch(1) |
NAME¶
hmmfetch - retrieve profile HMM(s) from a fileSYNOPSIS¶
hmmfetch [options] <hmmfile> <key>(retrieves HMM named <key>)
(retrieves all HMMs listed in <keyfile>)
(indexes <hmmfile> for fetching)
DESCRIPTION¶
Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam database, for example).% hmmfetch Pfam-A.hmm Caudal_act % hmmfetch Pfam-A.hmm PF00045
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.COPYRIGHT¶
@HMMER_COPYRIGHT@ @HMMER_LICENSE@
AUTHOR¶
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org
@HMMER_DATE@ | HMMER @HMMER_VERSION@ |