PROT.pl

#!/usr/bin/env perl
use Modern::Perl;

my %geneticCode = qw(
	UUU F      CUU L      AUU I      GUU V
	UUC F      CUC L      AUC I      GUC V
	UUA L      CUA L      AUA I      GUA V
	UUG L      CUG L      AUG M      GUG V
	UCU S      CCU P      ACU T      GCU A
	UCC S      CCC P      ACC T      GCC A
	UCA S      CCA P      ACA T      GCA A
	UCG S      CCG P      ACG T      GCG A
	UAU Y      CAU H      AAU N      GAU D
	UAC Y      CAC H      AAC N      GAC D
	UAA Stop   CAA Q      AAA K      GAA E
	UAG Stop   CAG Q      AAG K      GAG E
	UGU C      CGU R      AGU S      GGU G
	UGC C      CGC R      AGC S      GGC G
	UGA Stop   CGA R      AGA R      GGA G
	UGG W      CGG R      AGG R      GGG G
);

while (<>) {
	my @rna = ($_ =~ /.{3}/g);
	for (@rna) {
		print $geneticCode{$_} unless $geneticCode{$_} eq "Stop";
	}
	print "\n";
}