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.


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.


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).


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


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


User name for RAST access.


Password for RAST access.


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