proteins_to_functions

The routine proteins_to_functions allows users to access functions associated with specific protein sequences. The input proteins are given as a list of MD5 values (these MD5 values each correspond to a specific protein sequence). For each input MD5 value, a list of [feature-id,function] pairs is constructed and returned. Note that there are many cases in which a single protein sequence corresponds to the translation associated with multiple protein-encoding genes, and each may have distinct functions (an undesirable situation, we grant).

This function allows you to access all of the functions assigned (by all annotation groups represented in Kbase) to each of a set of sequences.

Example:

    proteins_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. For each input line there are multiple output lines, one for each fid the protein maps to. Two columns are added to each output line, a fid and a function.

Documentation for underlying call

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

  $return = $obj->proteins_to_functions($proteins)

Parameter and return types

$proteins is a proteins
$return is a reference to a hash where the key is a protein and the value is a fid_function_pairs
proteins is a reference to a list where each element is a protein
protein 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.