co_occurrence_evidence

co-occurence_evidence is used to retrieve the detailed pairs of genes that go into the computation of co-occurence scores. The scores reflect an estimate of the number of distinct OTUs that contain an instance of a co-occuring pair. This routine returns as evidence a list of all the pairs that went into the computation.

The input to the computation is table in which one of the columns contains co-occurring pairs. For example,

     echo 'kb|g.0.peg.101:kb|g.0.peg.263' | co_occurrence_evidence 

takes in a table with 1 column and one row. The input row is a single pair of related fids joined using a ':'.

The output is a table with an added (usually huge) column containing the evidence that the pair of fids are,in fact, related. The evidence is a comma-separated list of pairs (each pair being two fids joined with ':'). Thus the command above produces

           kb|g.0.peg.101:kb|g.0.peg.263        kb|g.0.peg.101:kb|g.0.peg.263,kb|g.10.peg.3334:kb|g.10.peg.3978,...

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 co_occurrence_evidence. It is documented as follows:

  $return = $obj->co_occurrence_evidence($pairs_of_fids)

Parameter and return types

$pairs_of_fids is a pairs_of_fids
$return is a reference to a list where each element is a reference to a list containing 2 items:
	0: a pair_of_fids
	1: an evidence
pairs_of_fids is a reference to a list where each element is a pair_of_fids
pair_of_fids is a reference to a list containing 2 items:
	0: a fid
	1: a fid
fid is a string
evidence is a reference to a list where each element is a pair_of_fids

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 an extra column (containing large evidence strings) added.

Input lines that cannot be extended are written to stderr.