NAME¶
cmpress - prepare a covariance model database for cmscan
SYNOPSIS¶
cmpress [options] <cmfile>
DESCRIPTION¶
Starting from a CM database
<cmfile> in standard Infernal-1.1
format, construct binary compressed datafiles for
cmscan. The
cmpress step is required for
cmscan to work.
The
<cmfile> must be have already been calibrated with
cmcalibrate for
cmpress to work.
Four files are created:
<cmfile>.i1m, <cmfile>.i1i,
<cmfile>.i1f, and
<cmfile>.i1p. The
<cmfile>.i1m file contains the covariance models, associated
filter p7 profile HMMs and their annotation in a binary format. The
<cmfile>.i1i file is an SSI index for the
<cmfile>.i1m file. The
<cmfile>.i1f file contains
precomputed data structures for the fast heuristic filter (the SSV filter) for
the filter p7 profile HMMs in
<cmfile>. The
<cmfile>.i1p file contains precomputed data structures for the
rest of each profile filter p7 HMM.
<cmfile> may not be '-' (dash); running
cmpress on a
standard input stream rather than a file is not allowed.
OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and all available
options.
- -F
- Force; overwrites any previous cmpress'ed datafiles. The default is to
bitch about any existing files and ask you to delete them first.
SEE ALSO¶
See
infernal(1) for a master man page with a list of all the individual
man pages for programs in the Infernal package.
For complete documentation, see the user guide that came with your Infernal
distribution (Userguide.pdf); or see the Infernal web page ().
COPYRIGHT¶
Copyright (C) 2014 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called
COPYRIGHT in your Infernal source distribution, or see the Infernal web page
().
AUTHOR¶
The Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org