p3-gto

Create GTO Files from PATRIC Genomes

p3-gto.pl [options] genome1 genome2 ... genomeN

This script creates GenomeTypeObject files for the specified PATRIC genomes. Each file is named using the genome ID with the suffix .gtoand placed in the current directory. The --outDir option can be used to specify an alternate output directory. Existing files will be replaced.

Parameters

The positional parameters are the IDs of the genomes to extract. A parameter of - indicates that the standard input contains a list of genome IDs to process. The options in Column Options can be used to specify the input column and Input Options can be used to modify the standard input.

In addition, the following command-line options can modify the default behavior.

outDir

Name of the directory in which to put the output files. (The default is the current working directory.)

missing

Only process genomes for which files do not yet exist in the output directory. The default is to replace existing files.