cmfetch - retrieve covariance model(s) from a file
cmfetch [options] <cmfile> <key>
(retrieves CM named <key>)
cmfetch -f [options] <cmfile> <keyfile>
(retrieves all CMs listed in <keyfile>)
cmfetch --index [options] <cmfile>
(indexes <cmfile> for fetching)
Retrieves one or more CMs from an <cmfile>
(a large Rfam database,
To enable very fast retrieval, index the <cmfile>
The index is a binary file named
The default mode is to retrieve a single CM by name or accession, called the
% cmfetch Rfam.cm tRNA
% cmfetch Rfam.cm RF00005
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
and any remaining data on the line is ignored. This allows
a variety of whitespace delimited datafiles to be used as
When using -f
and a <keyfile>,
been indexed, the keys are retrieved in the order they occur in the
but if <cmfile>
isn't indexed, keys are
retrieved in the order they occur in the <cmfile>.
This is a side
effect of an implementation that allows multiple keys to be retrieved even if
is a nonrewindable stream, like a standard input
In normal use (without --index
may be '-' (dash), which means reading input from
rather than a file. With the --index
may not be '-'; it does not make sense to index a
standard input stream. With the -f
option, either <cmfile>
(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 CM names or
accessions, then fetch them all to a new file, just with one command.
By default, the CM is printed to standard output in Infernal-1.1 format.
- Help; print a brief reminder of command line usage and all
- 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> (a CM
name or accession). Blank lines and comment lines (that start with a #
character) are ignored.
- -o <f>
- Output CM(s) to file <f> instead of to
- Output CM(s) to individual file(s) named <key>
instead of standard output. With the -f option, this can result in
many files being created.
- Instead of retrieving one or more profiles from
<cmfile>, index the <cmfile> for future
retrievals. This creates a <cmfile>.ssi binary index file.
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 (C) 2016 Howard Hughes Medical Institute.
Freely distributed under a BSD open source license.
For additional information on copyright and licensing, see the file called
COPYRIGHT in your Infernal source distribution, or see the Infernal web page
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