protein_families_to_functions

protein_families_to_functions can be used to extract the set of functions assigned to the fids that make up the family. Each input protein_family is mapped to a family function.

Example:

protein_families_to_functions [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 protein_families_to_functions. It is documented as follows:

$return = $obj->protein_families_to_functions($protein_families)

Parameter and return types

$protein_families is a protein_families
$return is a reference to a hash where the key is a protein_family and the value is a fid_function_pairs
protein_families is a reference to a list where each element is a protein_family
protein_family is a string
fid_function_pairs is a reference to a list where each element is a fid_function_pair
fid_function_pair is a reference to a list containing 2 items:
	0: a fid
	1: a function
fid is a string
function 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.