genomes_to_genome_data

Example:

genomes_to_genome_data [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_genome_data. It is documented as follows:

$return = $obj->genomes_to_genome_data($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_data
genomes is a reference to a list where each element is a genome
genome is a string
genome_data is a reference to a hash where the following keys are defined:
	complete has a value which is an int
	contigs has a value which is an int
	dna_size has a value which is an int
	gc_content has a value which is a float
	genetic_code has a value which is an int
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	taxonomy has a value which is a string
	genome_md5 has a value which 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 in this order: rnas gc_content dna_size taxonomy scientific_name contigs genome_md5 pegs genetic_code complete.

Input lines that cannot be extended are written to stderr.