otu_members

We deine the notion of OTU loosely. We try to keep genomes with 97% identical SSUrRNAs within the same OTU. We pick a representative genome for each OTU, and we try to keep all genomes that have 97% identical SSU rRNAs in the same OTU.

This command is intended to add a column containing the genomes from the same OTU.

Example:

otu_members [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 genome 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 otu_members. It is documented as follows:

$return = $obj->otu_members($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 reference to a hash where the key is a genome and the value is a genome_name
genomes is a reference to a list where each element is a genome
genome is a string
genome_name is a string

Command-Line Options

-c Column

This is used only if the column containing genome identifiers 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 (a genome from the same OTU) added. If there are N genomes in the OTU for the genome in an input line, then N output lines will be generated, each containing a single genome ID from the same OTU.

Input lines that cannot be extended are written to stderr.