subsystems_to_genomes

This command takes as input a table with a column containing subsystem names. An extra column is appended to the table containing genome IDs (for those genomes included in the subsystem with an active variant code (not matching /\*?(o|-1)/).

Example:

    subsystems_to_genomes [arguments] < input > output

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 the subsystem name. If another column contains the subsystem name use

    -c N

where N is the column (from 1) that contains the subsystem.

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

Documentation for underlying call

This script is a wrapper for the CDMI-API call subsystems_to_genomes. It is documented as follows:

  $return = $obj->subsystems_to_genomes($subsystems)

Parameter and return types

$subsystems is a subsystems
$return is a reference to a hash where the key is a subsystem and the value is a reference to a list where each element is a reference to a list containing 2 items:
	0: a variant
	1: a genome
subsystems is a reference to a list where each element is a subsystem
subsystem is a string
variant is a string
genome is a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with two extra columns added (the variant code and the genome).

Input lines that cannot be extended are written to stderr.