Man pages sections > man1 > cmfetch

cmfetch - retrieve covariance model(s) from a file

cmfetch(1) Infernal Manual cmfetch(1)


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, for example).
To enable very fast retrieval, index the <cmfile> first, using cmfetch --index. The index is a binary file named <cmfile>.ssi.
The default mode is to retrieve a single CM by name or accession, called the <key>. For example:
  % cmfetch tRNA
  % cmfetch 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 <key>, and any remaining data on the line is ignored. This allows a variety of whitespace delimited datafiles to be used as <keyfile>s.
When using -f and a <keyfile>, if <cmfile> has been indexed, the keys are retrieved in the order they occur in the <keyfile>, 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 the <cmfile> is a nonrewindable stream, like a standard input pipe.
In normal use (without --index or -f options), <cmfile> may be '-' (dash), which means reading input from stdin rather than a file. With the --index option, <cmfile> may not be '-'; it does not make sense to index a standard input stream. With the -f option, either <cmfile> or <keyfile> (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 available options.
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 standard output.
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.


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 (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 ().


The Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
July 2016 Infernal 1.1.2