fids_to_regulon_data

Example:

fids_to_regulon_data [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 identifer. If another column contains the identifier use

-c N

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

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 fids_to_regulon_data. It is documented as follows:

$return = $obj->fids_to_regulon_data($fids)

Parameter and return types

$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a regulons_data
fids is a reference to a list where each element is a fid
fid is a string
regulons_data is a reference to a list where each element is a regulon_data
regulon_data is a reference to a hash where the following keys are defined:
	regulon_id has a value which is a regulon
	regulon_set has a value which is a fids
	tfs has a value which is a fids
regulon 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 ]

-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: regulon_id, regulon_set, tfs.

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added.

Input lines that cannot be extended are written to stderr.