hmmfetch - retrieve profiles from a file
hmmfetch [options] hmmfile key
(retrieve HMM named key)
hmmfetch -f [options] hmmfile keyfile
(retrieve all HMMs listed in keyfile)
hmmfetch --index [options] hmmfile
(index hmmfile for fetching)
Quickly retrieves one or more profile HMMs from an hmmfile
(a large Pfam
database, for example).
For maximum speed, the hmmfile
should be indexed first, using hmmfetch
. The index is a binary file named hmmfile
this is optional, and retrieval will still work from unindexed files, albeit
much more slowly.
The default mode is to retrieve a single profile by name or accession, called
. 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 a keyfile
When using -f
and a keyfile
, if hmmfile
has been indexed,
the keys are retrieved in the order they occur in the keyfile
, but if
isn't indexed, keys are retrieved in the order they occur in
. This is a side effect of an implementation that allows
multiple keys to be retrieved even if the hmmfile
is a nonrewindable
stream, like a standard input pipe.
In normal use (without --index
be '-' (dash), which means reading input from stdin rather than a file. With
may not be '-'; it does not make
sense to index a standard input stream. With the -f
(but not both) may be '-'. It is often
particularly useful to read keyfile
from standard input, because this
allows use to use arbitrary command line invocations to create a list of HMM
names or accessions, then fetch them all to a new file, just with one command.
By default, fetched HMMs are 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 being
- Instead of retrieving one or more profiles from hmmfile, index the
hmmfile for future retrievals. This creates a hmmfile.ssi
binary index file.
(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 (http://hmmer.org/).
Copyright (C) 2018 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page