get_entity_PairSet

A PairSet is a precompute set of pairs or genes. Each pair occurs close to one another of the chromosome. We believe that all of the first members of the pairs correspond to one another (are quite similar), as do all of the second members of the pairs. These pairs (from prokaryotic genomes) offer on of the most powerful clues relating to uncharacterized genes/peroteins.

Example:

get_entity_PairSet -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 PairSet entity has the following relationship links:

IsDeterminedBy Pairing

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:

score

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.