svr_preferred_roles

Get preferred roles, translating functions into more acceptable forms

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Example:

    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.

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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 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.

-d

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).