In response to Tonu Margus's question, I posted some scripts.
The script "translate.fil" had an error in to and should
read as follows:
set begin = ` grep 'CDS' $1 | cut -c22-40 | cut -f1 -d"." `
set end = ` grep 'CDS' $1 | cut -c22-40 | cut -f2 -d" " | cut -c2-7 `
echo $begin, $end
translate $1 -default -beg=$begin -end=$end -out=$1.pep
This script will translate files that have a continuous reading frame.
Sorry for any inconvenience.