get_entity_Pairing

A pairing indicates that two features are found close together in a genome. Not all possible pairings are stored in the database; only those that are considered for some reason to be significant for annotation purposes.The key of the pairing is the concatenation of the feature IDs in alphabetical order with an intervening colon.

Example:

get_entity_Pairing -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 Pairing entity has the following relationship links:

Determines PairSet

IsPairOf Feature

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:

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.