get_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:

get_entity_Feature -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.

Related entities

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

-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:

feature_type

source_id

sequence_length

function

alias

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.