roles_to_protein_families

roles_to_protein_families can be used to locate the protein families containing features that have assigned functions implying that they implement designated roles. Note that for any input role (given as a role description), you may have a set of distinct protein_families returned.

Example:

roles_to_protein_families [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_protein_families. It is documented as follows:

$return = $obj->roles_to_protein_families($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 protein_families
roles is a reference to a list where each element is a role
role is a string
protein_families is a reference to a list where each element is a protein_family
protein_family 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.