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.