I know it's quite late but in case somebody else has the same question. Augustus has a bunch of scripts for the postprocessing in the installation directory under
augustus-x.x.x/scripts/. The basic parsing script is called
getAnnoFasta.pl and takes the resulting gtf/gff as the input and outputs two files, one with nucleotide fasta (
.codingseq) and the other one with protein fasta (
I guess you can find other useful scripts there as well.