p3-rast

Annotate a Genome Using RAST

p3-rast.pl [ options ] taxonID name

This script invokes the RAST service over the web to annotate a genome. It will submit a FASTA file to RAST, wait for the job to finish, and then format the results into a JSON-form GenomeTypeObject.

Parameters

The input can be a contig-only GenomeTypeObject in JSON format or a contig FASTA file. The two positional parameters are the proposed taxonomic ID and the genome name. The command-line options in Input Options are used to specify the standard input. The additional command-line options are as follows.

  • gto

If specified, then the input file is presumed to be a contig object or a workspace contig object encoded in JSON format. The contigs must be in the form of a list attached to the contigsmember or the contigs member of the data member (the latter indicating a workspace object).

  • domain

The domain of the new genome– B for bacteria, A for archaea, and so forth. The default is B.

  • geneticCode

The genetic code of the new genome. The default is 11.

  • user

User name for RAST access.

  • password

Password for RAST access.

  • sleep

Sleep interval in seconds while waiting for the job to complete. The default is 60.

  • noIndex

Do not add the genome to the BV-BRC index.