protein_families_to_co_occurring_families

Since we accumulate data relating to the co-occurrence (i.e., chromosomal clustering) of genes in prokaryotic genomes, we can note which pairs of genes tend to co-occur. From this data, one can compute the protein families that tend to co-occur (i.e., tend to cluster on the chromosome). This allows one to formulate conjectures for unclustered pairs, based on clustered pairs from the same protein_families.

Example:

    protein_families_to_co_occurring_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 protein_families_to_co_occurring_families. It is documented as follows:

  $return = $obj->protein_families_to_co_occurring_families($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 fc_protein_families
protein_families is a reference to a list where each element is a protein_family
protein_family is a string
fc_protein_families is a reference to a list where each element is a fc_protein_family
fc_protein_family is a reference to a list containing 3 items:
	0: a protein_family
	1: a score
	2: a function
score is a float
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.