Documentation read from 01/25/2012 11:58:34 version of /scratch/FIGdisk.server/FIG/bin/svr_function_of.

svr_function_of

svr_function_of

Get functions of protein-encoding genes

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Example:

    svr_all_features 3702.1 peg | svr_function_of

would produce a 2-column table. The first column would contain PEG IDs for genes occurring in genome 3702.1, and the second would contain the functions of those genes.

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The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the PEG for which functions are being requested. If some other column contains the PEGs, use

    -c N

where N is the column (from 1) that contains the PEG in each case.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Command-Line Options

-c Column

This is used only if the column containing PEGs is not the last.

-s

Strip comments from the functions.

-keep

This is used to keep input lines for which the PEG has no function

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (the function associated with the PEG).