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cmfetch(1) Infernal Manual cmfetch(1) NAME cmfetch - retrieve covariance model(s) from a file SYNOPSIS 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) DESCRIPTION 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 re- maining data on the line is ignored. This allows a variety of white- space 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 <cm- file>. 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 ac- cessions, 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 for- mat. OPTIONS -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 sin- gle _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 stan- dard output. --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 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 In- fernal distribution (Userguide.pdf); or see the Infernal web page (). COPYRIGHT Copyright (C) 2019 Howard Hughes Medical Institute. Freely distributed under the BSD open source license. For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal source distribution, or see the In- fernal web page (). AUTHOR The Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org Infernal 1.1.3 Nov 2019 cmfetch(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR
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