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

svr_role_to_pegs [-c column] [-g Genomes] < Roles > with.PEGs

svr_role_to_pegs [-c column] [-g Genomes] < Roles > with.PEGs

Get PEGs that implement a given set of functional roles


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 a role for which functions are being requested. If some other column contains the roles, use

    -c N

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

If you wish to constrain the set of PEGs to a specific set of genomes, you can specify a file containing genomes IDs.

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.

-g Genomes

This is a file containing a genome ID in column 1 (use cut -fn to make the file if necessary).

Output Format

The output file is a copy of the table from the input, except that an extra column giving a PEG id is appended (and many lines in the output may result from a single input line).