p3-mass-cluster-run

Mass Cluster Run

p3-mass-cluster-run.pl [options] workDir outDir

This is a special-purpose script that processes the genus-species file from p3-genus-species as input and creates signature cluster information for each species listed.

Parameters

The positional parameters are the name of the working directory and the name of the output directory. The working directory will contain temporary files built by the clustering script. The output directory will contain a file called genus.species.clusters.htmlcontaining the cluster data for the specified genus and species.

The standard input can be overridden using the options in Input Options. The first column must contain genus names and the second species names.

The additional command-line options are as follows.

• size

The size of each sample set when computing clusters. The default is 20.

• iterations

The number of sampling iterations to run. The default is 4.

• min

The minimum portion of occurrences for a protein family to be considered significant. The default is 0.8.

• max

The maximum portion of occurrences for a protein family to be considered insignificant. The default is 0.1.

• resume

If specified, genus-species combinations will be skipped if output files already exist.