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cmfetch - Online in the Cloud

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This is the command cmfetch that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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

% 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 <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.


-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> (a CM name
or accession). Blank lines and comment lines (that start with a # character) are

-o <f> Output CM(s) to file <f> instead of to standard output.

-O 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.

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