Documentation read from 04/17/2019 22:07:28 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_subsystem_genome_data.



    svr_subsystem_genome_data --genomeFile=genomes.tbl <sub_ids.tbl >sub_data.tbl

Output the features, variants, and roles for one or more subsystems, optionally filtered by genome ID.

This script takes as input a tab-delimited file with subsystem IDs at the end of each line. For each subsystem ID, numerous output lines are produced describing the contents of the subsystem. Each line will consist of

  1. Subsystem ID
  2. Genome ID (possibly with a region code)
  3. Code for the variant of this subsystem used by the genome.
  4. ID of a subsystem role.
  5. ID of a feature performing the role.

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

Command-Line Options


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


Column index. If specified, indicates that the input subsystem IDs should be taken from the indicated column instead of the last column. The first column is column 1.


If specified, the name of a tab-delimited file containing genome IDs in the last column. Only data relating to the specified genomes will be included in the output.