Provided by: infernal_1.1.2-2_amd64
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 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 ignored. -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. --index 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 ().
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