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

query_entity_Feature

Query the entity Feature.

A feature (sometimes also called a gene) is a part of a genome that is of special interest. Features may be spread across multiple DNA sequences (contigs) of a genome, but never across more than one genome. Each feature in the database has a unique ID that functions as its ID in this table. Normally a Feature is just a single contigous region on a contig. Features have types, and an appropriate choice of available types allows the support of protein-encoding genes, exons, RNA genes, binding sites, pathogenicity islands, or whatever.

Example:

query_entity_Feature -a

The Feature entity has the following relationship links:

Controls CoregulatedSet
Encompasses Feature
HasCoregulationWith Feature
HasFunctional Role
HasIndicatedSignalFrom Experiment
HasLevelsFrom ProbeSet
IsAnnotatedBy Annotation
IsContainedIn SSCell
IsCoregulatedWith Feature
IsEncompassedIn Feature
IsExemplarOf Role
IsFormedInto AtomicRegulon
IsInPair Pairing
IsLocatedIn Contig
IsMemberOf Family
IsOwnedBy Genome
IsRegulatedIn CoregulatedSet
Produces ProteinSequence

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:

feature_type
source_id
sequence_length
function
alias

Output Format

The standard output is a tab-delimited file containing a column for each requested field.