regulons_to_fids

The CS contains two similar notions:

1. atomic regulons, which are sets of fids thought to have exactly the
   same expression profiles (derived from operons, subsystems, and expression data)

2. regulons which are thought of as a set of genes impacted by a transcription factor.
   This second notion is built up looking for binding-site/transcription-factor pairs 
   and reconciling the insights with operons and subsystems.

Clearly the two notions are closely related.

This command takes as input a table in which one column is composed of regulon ids, and it adds a column corresponding to the fids that make up the regulon.

Example:

regulons_to_fids [arguments] < input > output

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 regulon identifer. If another column contains the identifier use

-c N

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

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

Documentation for underlying call

This script is a wrapper for the CDMI-API call regulons_to_fids. It is documented as follows:

$return = $obj->regulons_to_fids($regulons)

Parameter and return types

$regulons is a regulons
$return is a reference to a hash where the key is a regulon and the value is a fids
regulons is a reference to a list where each element is a regulon
regulon is a string
fids is a reference to a list where each element is a fid
fid is a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column (fids in the regulon) added.

Input lines that cannot be extended are written to stderr.