fids_to_co_occurring_fids

One of the most powerful clues to function relates to conserved clusters of genes on the chromosome (in prokaryotic genomes). We have attempted to record pairs of genes that tend to occur close to one another on the chromosome. To meaningfully do this, we need to construct similarity-based mappings between genes in distinct genomes. We have constructed such mappings for many (but not all) genomes maintained in the Kbase CS. The prokaryotic geneomes in the CS are grouped into OTUs by ribosomal RNA (genomes within a single OTU have SSU rRNA that is greater than 97% identical). If two genes occur close to one another (i.e., corresponding genes occur close to one another), then we assign a score, which is the number of distinct OTUs in which such clustering is detected. This allows one to normalize for situations in which hundreds of corresponding genes are detected, but they all come from very closely related genomes.

The significance of the score relates to the number of genomes in the database. We recommend that you take the time to look at a set of scored pairs and determine approximately what percentage appear to be actually related for a few cutoff values.

Example:

fids_to_co_occurring_fids [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 fids_to_co_occurring_fids. It is documented as follows:

$return = $obj->fids_to_co_occurring_fids($fids)

Parameter and return types

$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a scored_fids
fids is a reference to a list where each element is a fid
fid is a string
scored_fids is a reference to a list where each element is a scored_fid
scored_fid is a reference to a list containing 2 items:
	0: a fid
	1: a float

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. For each line of input there may be multiple lines of output, one for each co_occuring fid. Two columns are added, the score and the co_occurring fid.

Input lines that cannot be extended are written to stderr.