svr_pegs_in_subsystems

    svr_pegs_in_subsystems genome_ids.tbl <subsystem_ids.tbl >peg_role_data.tbl

Return all genes in one or more subsystems found in one or more genomes.

This script takes a list of genomes and a list of subsystems and returns a list of the genes represented in each genome/subsystem pair. It takes one positional parameter-- the name of the file containing the genome IDs, and reads the list of subsystem IDs from the standard input.

The standard output will be a tab-delimited file, each record containing a subsystem ID, a functional role in that subsystem, and the ID of a gene with that role from one of the supplied genomes.

This is a pipe command. The input is from the standard input and the output is to the standard output.

The following command-line options are supported.

group

If specified, then each output line will be for a single role, and the gene IDs will be listed as a single comma-delimited string.

noroles

If specified, then the second column in each output line (functional role) will be omitted from the output.

url

The URL for the Sapling server, if it is to be different from the default.

c

Number (1-based) of the column in the input file containing the subsystem name. If omitted, the last column is used.