If translation takes place, it is always done according to the input file's default genetic code. If a genetic element has fragments, they will be reported in the result file. Otherwise, fragments are reported separately in the result file. This behaviour is irrespective of whether or not translation takes place. To do this, use -t.
Pepper can report the DNA sequence of each exon and intron separately.
To do this, use -ti. To do this, use -tw. The output file is list of intergenic sequences, one contig for each. Also, the line numbers of the original masterfile are maintained. Each non-coding region in the masterfile will be in a separate contig.