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

svr_neighborhood_of_role -r 2 < file.with.roles > with.added.role

svr_neighborhood_of_role -r 2 < file.with.roles > with.added.role

Find roles in metabolic-function neighborhood



    svr_neighborhood_of_roles < > with.steps.and.role.column.added

would take as input a file in which the last column was functional roles. Two columns would be added

    steps       is the number of steps traversed to reach the neighbor
    neighbor    is the neighboring role


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 relevant clusters are desired. If some other column contains the roles, use

    -c N

where N is the column (from 1) that contains the role 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 roles is not the last.

-r MaxSteps [default is 2]

This parameter gives the maximum number of steps (i.e., the "radius") the program can take to create the neighborhood of a role

Output Format

The standard output is a tab-delimited file. It consists of the input file with two extra columns added. The extra columns will contain the number of steps to the neighbor, along with the neighbor.