equiv_sequence_assertions

Different groups have made assertions of function for numerous protein sequences. The equiv_sequence_assertions allows the user to gather function assertions from all of the sources. Each assertion includes a field indicating whether the person making the assertion viewed themself as an "expert". The routine gathers assertions for all proteins having identical protein sequence.

Example:

    equiv_sequence_assertions [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 a protein identifier (i.e., an md5 value). If another column contains the md5s use

    -c N

where N is the column (from 1) that contains the protein identifiers.

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 equiv_sequence_assertions. It is documented as follows:

  $return = $obj->equiv_sequence_assertions($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 function_assertions
proteins is a reference to a list where each element is a protein
protein is a string
function_assertions is a reference to a list where each element is a function_assertion
function_assertion is a reference to a list containing 4 items:
	0: an id
	1: a function
	2: a source
	3: an expert
id is a string
function is a string
source is a string
expert is a string

Command-Line Options

-c Column

This is used only if the column containing the md5s 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 (identifier,source,function,expert).

Input lines that cannot be extended are written to stderr.