#!C:/STRAWB~1/perl/bin/perl.exe -w
use strict;
use warnings;

my $proteinfile = "Protein";

print "Enter a file containing DNA or RNA:\n\n";

my $DNA = <STDIN>;
chomp $DNA;

if(-f $DNA)
{
  local $/=undef;
  open(DNAFILE, $DNA) or die "ERROR open File: $DNA ($!)\n";
  $DNA = <DNAFILE>;
  close DNAFILE;
}
else
{
  print "File not found\n";
  print "using \"$DNA\" as sequence \n\n";
}
$DNA =~ s/\s//g;

#Überprüfen ob file DNA oder RNA enthält
my $i_DNA = $DNA=~tr/ACTG//;
my $i_RNA = $DNA=~tr/U//;
my $i_RNA += $i_DNA; #Da die RNA aus allen U plus den anderen Basen besteht

#wenn nun $i nicht der Länge der Sequenz entspricht, war mindestens 1 Element kein Nukleotid
if($i_DNA == length $DNA)
{ print "Sequence successfully identified as DNA\n\n"; }
elsif($i_RNA == length $DNA)
{ print "Sequence succesfully identified as RNA\n\n"; }
else
{
  print "Sequence is whether DNA nor RNA\n\n";
  print "cannot continue!\n\n";
  exit();
}



#DNA wird in RNA umgeschrieben
(my $RNA = $DNA) =~ s/T/U/ig;

#print "The RNA sequence is:\n\n";
#print "$RNA\n\n";

#unpack kann auch als alternative zu split verwendet werden wobei dann "A1" x length $RNA benutzt würde
my @triplets = unpack("A3" x (length ($RNA)/3), $RNA);


#Initialisierung der CODONS
my %CODONS=();
my %TRIPLETS=();
$CODONS{ala}={letter=>'A', count=>0};
  $TRIPLETS{GCU}=$CODONS{ala};
  $TRIPLETS{GCC}=$CODONS{ala};
  $TRIPLETS{GCA}=$CODONS{ala};
  $TRIPLETS{GCG}=$CODONS{ala};
$CODONS{cys}={letter=>'C', count=>0};
  $TRIPLETS{UGU}=$CODONS{cys};
  $TRIPLETS{UGC}=$CODONS{cys};
$CODONS{asp}={letter=>'D', count=>0};
  $TRIPLETS{GAU}=$CODONS{asp};
  $TRIPLETS{GAG}=$CODONS{asp};
$CODONS{glu}={letter=>'E', count=>0};
  $TRIPLETS{GAA}=$CODONS{glu};
  $TRIPLETS{GAG}=$CODONS{glu};
$CODONS{phe}={letter=>'F', count=>0};
  $TRIPLETS{UUU}=$CODONS{phe};
  $TRIPLETS{UUC}=$CODONS{phe};
$CODONS{gly}={letter=>'G', count=>0};
  $TRIPLETS{GGU}=$CODONS{gly};
  $TRIPLETS{GGC}=$CODONS{gly};
  $TRIPLETS{GGA}=$CODONS{gly};
  $TRIPLETS{GGG}=$CODONS{gly};
$CODONS{his}={letter=>'H', count=>0};
  $TRIPLETS{CAU}=$CODONS{his};
  $TRIPLETS{CAC}=$CODONS{his};
$CODONS{ile}={letter=>'I', count=>0};
  $TRIPLETS{AUU}=$CODONS{ile};
  $TRIPLETS{AUC}=$CODONS{ile};
  $TRIPLETS{AUA}=$CODONS{ile};
$CODONS{lys}={letter=>'K', count=>0};
  $TRIPLETS{AAA}=$CODONS{lys};
  $TRIPLETS{AAG}=$CODONS{lys};
$CODONS{leu}={letter=>'L', count=>0};
  $TRIPLETS{CUU}=$CODONS{leu};
  $TRIPLETS{CUC}=$CODONS{leu};
  $TRIPLETS{CUA}=$CODONS{leu};
  $TRIPLETS{CUG}=$CODONS{leu};
  $TRIPLETS{UUA}=$CODONS{leu};
  $TRIPLETS{UUG}=$CODONS{leu};
$CODONS{met}={letter=>'M', count=>0};
  $TRIPLETS{AUG}=$CODONS{met};
$CODONS{asn}={letter=>'N', count=>0};
  $TRIPLETS{AAU}=$CODONS{asn};
  $TRIPLETS{AAC}=$CODONS{asn};
$CODONS{pro}={letter=>'P', count=>0};
  $TRIPLETS{CCU}=$CODONS{pro};
  $TRIPLETS{CCC}=$CODONS{pro};
  $TRIPLETS{CCA}=$CODONS{pro};
  $TRIPLETS{CCG}=$CODONS{pro};
$CODONS{gln}={letter=>'Q', count=>0};
  $TRIPLETS{CAA}=$CODONS{gln};
  $TRIPLETS{CAG}=$CODONS{gln};
$CODONS{arg}={letter=>'R', count=>0};
  $TRIPLETS{CGU}=$CODONS{arg};
  $TRIPLETS{CGC}=$CODONS{arg};
  $TRIPLETS{CGA}=$CODONS{arg};
  $TRIPLETS{CGG}=$CODONS{arg};
  $TRIPLETS{AGA}=$CODONS{arg};
  $TRIPLETS{AGG}=$CODONS{arg};
$CODONS{ser}={letter=>'S', count=>0};
  $TRIPLETS{AGU}=$CODONS{ser};
  $TRIPLETS{AGC}=$CODONS{ser};
  $TRIPLETS{UCU}=$CODONS{ser};
  $TRIPLETS{UCC}=$CODONS{ser};
  $TRIPLETS{UCA}=$CODONS{ser};
  $TRIPLETS{UCG}=$CODONS{ser};
$CODONS{thr}={letter=>'T', count=>0};
  $TRIPLETS{ACU}=$CODONS{thr};
  $TRIPLETS{ACC}=$CODONS{thr};
  $TRIPLETS{ACA}=$CODONS{thr};
  $TRIPLETS{ACG}=$CODONS{thy};
$CODONS{val}={letter=>'V', count=>0};
  $TRIPLETS{GUU}=$CODONS{val};
  $TRIPLETS{GUC}=$CODONS{val};
  $TRIPLETS{GUA}=$CODONS{val};
  $TRIPLETS{GUG}=$CODONS{val};
$CODONS{trp}={letter=>'W', count=>0};
  $TRIPLETS{UUG}=$CODONS{trp};
$CODONS{tyr}={letter=>'Y', count=>0};
  $TRIPLETS{UAU}=$CODONS{tyr};
  $TRIPLETS{UAC}=$CODONS{tyr};
$CODONS{stop}={letter=>'!STOP!', count=>0};
  $TRIPLETS{UAA}=$CODONS{stop};
  $TRIPLETS{UAG}=$CODONS{stop};
  $TRIPLETS{UGA}=$CODONS{stop};
  $TRIPLETS{UGG}=$CODONS{stop};

#Jedes Triplet wird nun ausgetauscht durch den 1-lettercode seiner Aminosäure
foreach $trip (@triplets)
{
  $TRIPLETS{uc($trip)}->{count}++;
  $trip = $TRIPLETS{uc($trip)}->{letter};
}

#Berechnung des prozentualen Vorkommen jeder Aminosäure
my $tot = keys(%CODONS);
$trip->{percent}=$_->{count}/$tot*100 for (values(%CODONS));

#Das ganze wird auf das File Protein geschrieben
open(PROTEINFILE , '>', $proteinfile) or die("ERROR open file ($proteinfile) ($!)\n");
print PROTEINFILE join( " " ,@triplets)."\n\n";
for (keys(%CODONS))
{ printf PROTEINFILE "%s = %1.2f%\n\n", $_, $CODONS{$_}->{percent}; }
close PROTEINFILE;

print "Proteinsequence written on 'Protein'\n\n";