genomes_to_taxonomies

The routine genomes_to_taxonomies can be used to retrieve taxonomic information for each of a list of input genomes. For each genome in the input list of genomes, a list of taxonomic groups is returned. Kbase will use the groups maintained by NCBI. For an NCBI taxonomic string like

cellular organisms;
Bacteria;
Proteobacteria;
Gammaproteobacteria;
Enterobacteriales;
Enterobacteriaceae;
Escherichia;
Escherichia coli

associated with the strain 'Escherichia coli 1412', this routine would return a list of these taxonomic groups:

['Bacteria',
 'Proteobacteria',
 'Gammaproteobacteria',
 'Enterobacteriales',
 'Enterobacteriaceae',
 'Escherichia',
 'Escherichia coli',
 'Escherichia coli 1412'
]

That is, the initial "cellular organisms" has been deleted, and the strain ID has been added as the last "grouping".

The output is a mapping from genome IDs to lists of the form shown above.

Example:

genomes_to_taxonomies [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_taxonomies. It is documented as follows:

$return = $obj->genomes_to_taxonomies($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 taxonomic_groups
genomes is a reference to a list where each element is a genome
genome is a string
taxonomic_groups is a reference to a list where each element is a taxonomic_group
taxonomic_group 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. One extra column is added, consisting of the taxonomy list presented as a single string with items separated by a ":".

Input lines that cannot be extended are written to stderr.