p3-user-subsystem

Create a Spreadsheet for a Custom Subsystem

p3-user-subsystem.pl [options] featureGroup1 featureGroup2 ... featureGroupN

This script takes as input the names of one or more feature groups and builds a subsystem spreadsheet. The spreadsheet is output in both tab-delimited and HTML formats.

The features listed in the feature groups define subsystem variants. The subsystem may then be projected onto each genome in an optionally-specified genome group. Projection is done using protein families.

Parameters

The positional parameters are the name of the subsystem and the names or one or more feature groups.

The command-line options are the following

  • outDir

The name of an output directory into which the output files spreadsheet.txt and spreadsheet.html will be written. The default is the current directory.

  • genomes

The name of a genome group. If specified, the subsystem will be projected onto the genomes in this group.