Documentation read from 04/17/2019 22:07:27 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_preferred_roles.



Get preferred roles, translating functions into more acceptable forms



    echo 83333.1 | svr_all_features peg | svr_function_of | svr_preferred_roles | cut -f1,3

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 preferred functions of those genes.


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 function to be translated. If the last column does not contain it, then

    -c N

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

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 functions is not the last.


This is used to print only lines in which the original and translated functions differ.

Output Format

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