genomes_to_subsystems

A user can invoke genomes_to_subsystems to rerieve the names of the subsystems relevant to each genome. The input is a list of genomes. The output is a mapping from genome to a list of 2-tuples, where each 2-tuple give a variant code and a subsystem name. Variant codes of -1 (or *-1) amount to assertions that the genome contains no active variant. A variant code of 0 means "work in progress", and presence or absence of the subsystem in the genome should be undetermined.

Example:

    genomes_to_subsystems [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 identifer. If another column contains the identifier 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 genomes_to_subsystems. It is documented as follows:

  $return = $obj->genomes_to_subsystems($genomes)

Parameter and return types

$genomes is a genomes
$return is a reference to a hash where the key is a genome and the value is a variant_subsystem_pairs
genomes is a reference to a list where each element is a genome
genome is a string
variant_subsystem_pairs is a reference to a list where each element is a variant_of_subsystem
variant_of_subsystem is a reference to a list containing 2 items:
	0: a subsystem
	1: a variant
subsystem is a string
variant 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. For each line of the input file there can be many output files, one per subsystem. A single field of variant,subsystem is added to the end of each line.

Input lines that cannot be extended are written to stderr.