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

Find roles in metabolic-function neighborhood

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Example:

    svr_neighborhood_of_roles < roles.in.file > 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

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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 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.