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Bio-KBase-0.06
River stage zero No dependents
/ er_scripts/query_entity_Genome

query_entity_Genome

Query the entity Genome.

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:

query_entity_Genome -a

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

-is field,value

Limit the results to entities where the given field has the given value.

-like field,value

Limit the results to entities where the given field is LIKE (in the sql sense) the given value.

-op operator,field,value

Limit the results to entities where the given field is related to the given value based on the given operator.

The operators supported are as follows. We provide text based alternatives to the comparison operators so that extra quoting is not required to keep the command-line shell from confusing them with shell I/O redirection operators.

< or lt
> or gt
<= or le
>= or ge
=
LIKE
-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 containing a column for each requested field.