representative

Genomes within KBase have been grouped into OTUs. Usually, members of the same OTU have SSU RNAs that are 97% or more identical, and usually two genomes with 97% identical SSU RNAs are part of the same OTU. However, we do not guarantee either assertion, and there are some genomes that have not been placed into OTUs (usually due to a missing or truncated rRNA).

Example:

representative [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 genome identifer. If another column contains the genome identifier use

-c N

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

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 representative. It is documented as follows:

$return = $obj->representative($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 genome
genomes is a reference to a list where each element is a genome
genome is a string

Command-Line Options

-c Column

This is used only if the column containing the genome IDs 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 an extra column added (the ID of the representative genome).

Input lines that cannot be extended are written to stderr.