roles_to_proteins

roles_to_proteins can be used to extract the set of proteins (designated by MD5 values) that currently are believed to implement a given role. Note that the proteins may be multifunctional, meaning that they may be implementing other roles, as well.

Example:

roles_to_proteins [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 roles_to_proteins. It is documented as follows:

$return = $obj->roles_to_proteins($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 proteins
roles is a reference to a list where each element is a role
role is a string
proteins is a reference to a list where each element is a protein
protein 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. For each input line there can be multiple output lines, one per protein associated with the role. Two extra columns are added to the output, function and protein.

Input lines that cannot be extended are written to stderr.