p3-project-subsystems¶

Project Subsystems onto PATRIC Genomes¶

gto_project.pl [ options ] outDir genome1 genome2 ... genomeN

This script will examine PATRIC genomes and project subsystems onto them. The resulting GTOs will be output to the specified output directory.

The positional parameters are the name of the output directory followed by one or more PATRIC genome IDs.

The command-line options are the following:

roleFile

Name of a tab-delimited file containing [role checksum, subsystem name] pairs.

variantFile

Name of a tab-delimited file containing in each record (0) a subsystem name, (1) a variant code, and (2) a space-delimited list of role checksums.