p3-gto-scan

Analyze Genome Typed Objects

p3-gto-scan.pl [options] gto1 gto2 ... gtoN

This script produces a report about the role profile of one or more GenomeTypeObject instances. The GTOs must be provided as files in JSON format. Each role will be converted to an MD5 role ID and counted. The counts are then compared. Finally, there will be statistics on the number of features and the DNA sequence length. These are normally placed at the end of the report, but can be rerouted to the standard error output.

Status of the script is written to the standard error output. The standard output contains the actual report.

Parameters

The positional parameters are the names of the GTO files. There must be at least one (although a comparison of one is trivial and just gives you a summary of the one). All files must encode the GTO in JSON format. (This is consistent with the output from p3-rast and p3-gto.)

The command-line options are those in Delimiter Options plus the following.

  • features

If specified, the features containing each role will be listed on the output.

  • peg

If specified, only protein-encoding features will be processed.

  • verbose

If specified, all roles will be displayed, rather than only the roles that differ between genomes.