roles_to_complexes

roles_to_complexes allows a user to connect Roles to Complexes, from there, the connection exists to Reactions (although in the actual ER-model model, the connection from Complex to Reaction goes through ReactionComplex). Since Roles also connect to fids, the connection between fids and Reactions is induced.

Example:

    roles_to_complexes [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. For each line of input there may be multiple lines of output, one per complex associated with the role. Two columns are appended to the input line, the optional flag, and the complex id.

Documentation for underlying call

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

  $return = $obj->roles_to_complexes($roles)

Parameter and return types

$roles is a roles
$return is a reference to a hash where the key is a role and the value is a complexes
roles is a reference to a list where each element is a role
role is a string
complexes is a reference to a list where each element is a complex
complex 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 extra columns added.

Input lines that cannot be extended are written to stderr.