subsystems_to_fids

This command gives to access to all of the rows in a subsystem. It does not support selecting just rows for specific genomes (although the underlying API routine subsystems_to_fids does). This command gives you all of the

[genome,variant-code,fids]

for an input subsystem.

Example:

subsystems_to_fids [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 a subssytem name. If another column contains the subsystem 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_fids. It is documented as follows:

$return = $obj->subsystems_to_fids($subsystems, $genomes)

Parameter and return types

$subsystems is a subsystems
$genomes is a genomes
$return is a reference to a hash where the key is a subsystem and the value is a reference to a hash where the key is a genome and the value is a reference to a list containing 2 items:
	0: a variant
	1: a fids
subsystems is a reference to a list where each element is a subsystem
subsystem is a string
genomes is a reference to a list where each element is a genome
genome is a string
variant is a string
fids is a reference to a list where each element is a fid
fid 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 extra columns added. These will be [Genome,Variant,FIF] (i.e., three columns are appended).

Input lines that cannot be extended are written to stderr.