all_entities_Genome

Return all instances of the Genome entity.

The Kbase houses a large and growing set of genomes. We often have multiple genomes that have identical DNA. These usually have distinct gene calls and annotations, but not always. We consider the Kbase to be a framework for managing hundreds of thousands of genomes and offering the tools needed to support compartive analysis on large sets of genomes, some of which are virtually identical. Each genome has an MD5 value computed from the DNA that is associated with the genome. Hence, it is easy to recognize when you have identical genomes, perhaps annotated by distinct groups.

Example:

    all_entities_Genome -a 

would retrieve all entities of type Genome and include all fields in the entities in the output.

Related entities

The Genome entity has the following relationship links:

HadResultsProducedBy ProbeSet

HasRepresentativeOf Family

IsCollectedInto OTU

IsComposedOf Contig

IsConfiguredBy AtomicRegulon

IsInTaxa TaxonomicGrouping

IsModeledBy Model

IsOwnerOf Feature

IsReferencedBy ObservationalUnit

Uses SSRow

WasSubmittedBy Source

Command-Line Options

-a

Return all fields.

-h

Display a list of the fields available for use.

-fields field-list

Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:

pegs

rnas

scientific_name

complete

prokaryotic

dna_size

contigs

domain

genetic_code

gc_content

phenotype

md5

source_id

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. Input lines that cannot be extended are written to stderr.