reactions_to_complexes

Reactions are thought of as being either spontaneous or implemented by one or more Complexes. Complexes connect to Roles. Hence, the connection of fids or roles to reactions goes through Complexes.

Complexes are best thought of as things like the ribosome or ATP synthase, but when a single protein is not grouped with others, we still think of it as a complex made up of a single member.

Example:

reactions_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 reaction 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 reactions_to_complexes. It is documented as follows:

$return = $obj->reactions_to_complexes($reactions)

Parameter and return types

$reactions is a reactions
$return is a reference to a hash where the key is a reaction and the value is a complexes
reactions is a reference to a list where each element is a reaction
reaction 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 an extra column (the complex ID) added.

Input lines that cannot be extended are written to stderr.