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Bio-KBase-0.06
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/ er_scripts/get_entity_Genome

get_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:

get_entity_Genome -a < ids > table.with.fields.added

would read in a file of ids and add a column for each filed in the entity.

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 id. If some other column contains the id, use

-c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

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

-c Column

Use the specified column to define the id of the entity to retrieve.

-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.