#!C:/STRAWB~1/perl/bin/perl.exe -w

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

$DNA = <STDIN>;
chomp $DNA;

unless(open(DNAFILE, $DNA)){
                     print "File not found\n\n";
}

@DNA = <DNAFILE>;

$DNA = join('',@DNA);
$DNA =~ s/\s//g;


#Überprüfen ob file DNA oder RNA enthält

@BASE_DNA = ("A","C","T","G");

#Für jedes Element wird nun überprüft, ob es einem Nukleotid entspricht,
#jedesmal, wenn die Bedingung erfüllt ist wird der count von $i erhöht
#Dabei wird bei jedem U, das im String vorkommt der RNA-count um 1 erhöht
for($pos = 0; $pos < length $DNA; ++$pos){
         $place = substr($DNA, $pos, 1);
         if(grep {$place eq $_} @BASE_DNA){
         ++$i_DNA;
         }
         elsif($place =~ /U/){
         ++$i_RNA;
         }
}


$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 eq length $DNA){
      print "Sequence successfully identified as DNA\n\n";
}
elsif($i_RNA eq length $DNA){
      print "Sequence succesfully identified as RNA\n\n";
}
else {
      print "Sequence is whether DNA nor RNA\n\n";
}



#DNA wird in RNA umgeschrieben
$RNA = $DNA;
$RNA =~ 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 $RNA benutzt würde
@triplets = unpack("A3" x (length ($RNA)/3), $RNA);



#Initialisierung der CODONS
@Ala = ("GCU","GCC","GCA","GCG");
@Cys = ("UGU","UGC");
@Asp = ("GAU","GAC");
@Glu = ("GAA","GAG");
@Phe = ("UUU","UUC");
@Gly = ("GGU","GGC","GGA","GGG");
@His = ("CAU","CAC");
@Ile = ("AUU","AUC","AUA");
@Lys = ("AAA","AAG");
@Leu = ("CUU","CUC","CUA","CUG","UUA","UUG");
@Met = ("AUG");
@Asn = ("AAU","AAC");
@Pro = ("CCU","CCC","CCA","CCG");
@Gln = ("CAA","CAG");
@Arg = ("CGU","CGC","CGA","CGG","AGA","AGG");
@Ser = ("AGU","AGC","UCU","UCC","UCA","UCG");
@Thr = ("ACU","ACC","ACA","ACG");
@Val = ("GUU","GUC","GUA","GUG");
@Trp = ("UGG");
@Tyr = ("UAU","UAC");
@STOP = ("UAA","UAG","UGA","UGG");


#Jedes Triplet wird nun ausgetauscht durch den 1-lettercode seiner Aminosäure
foreach $trip (@triplets){
                   if(grep{$trip eq $_} @Ala){
                   $trip = A;
                   ++$ala;
                   }
                   elsif(grep{$trip eq $_} @Cys){
                   $trip = C;
                   ++$cys
                   }
                   elsif(grep{$trip eq $_} @Asp){
                   $trip = D;
                   ++$asp;
                   }
                   elsif(grep{$trip eq $_} @Glu){
                   $trip = E;
                   ++$glu
                   }
                   elsif(grep{$trip eq $_} @Phe){
                   $trip = F;
                   ++$phe;
                   }
                   elsif(grep{$trip eq $_} @Gly){
                   $trip = G;
                   ++$gly;
                   }
                   elsif(grep{$trip eq $_} @His){
                   $trip = H;
                   ++$his
                   }
                   elsif(grep{$trip eq $_} @Ile){
                   $trip = I;
                   ++$ile
                   }
                   elsif(grep{$trip eq $_} @Lys){
                   $trip = K;
                   ++$lys;
                   }
                   elsif(grep{$trip eq $_} @Leu){
                   $trip = L;
                   ++$leu;
                   }
                   elsif(grep{$trip eq $_} @Met){
                   $trip = M;
                   ++$met;
                   }
                   elsif(grep{$trip eq $_} @Asn){
                   $trip = N;
                   ++$asn;
                   }
                   elsif(grep{$trip eq $_} @Pro){
                   $trip = P;
                   ++$pro;
                   }
                   elsif(grep{$trip eq $_} @Gln){
                   $trip = Q;
                   ++$gln;
                   }
                   elsif(grep{$trip eq $_} @Arg){
                   $trip = R;
                   ++$arg;
                   }
                   elsif(grep{$trip eq $_} @Ser){
                   $trip = S;
                   ++$ser;
                   }
                   elsif(grep{$trip eq $_} @Thr){
                   $trip = T;
                   ++$thr;
                   }
                   elsif(grep{$trip eq $_} @Val){
                   $trip = V;
                   ++$val;
                   }
                   elsif(grep{$trip eq $_} @Trp){
                   $trip = W;
                   ++$trp;
                   }
                   elsif(grep{$trip eq $_} @Tyr){
                   $trip = Y;
                   ++$tyr
                   }
                   elsif(grep{$trip eq $_} @STOP){
                   $trip = "!STOP!";
                   }
                   
}

#Berechnung des prozentualen Vorkommen jeder Aminosäure
$tot = @triplets;


$ALA = $ala / $tot * 100;
$CYS = $cys / $tot * 100;
$ASP = $asp / $tot * 100;
$GLU = $glu / $tot * 100;
$PHE = $phe / $tot * 100;
$GLY = $gly / $tot * 100;
$HIS = $his / $tot * 100;
$ILE = $ile / $tot * 100;
$LYS = $lys / $tot * 100;
$LEU = $leu / $tot * 100;
$MET = $met / $tot * 100;
$ASN = $asn / $tot * 100;
$PRO = $pro / $tot * 100;
$GLN = $gln / $tot * 100;
$ARg = $arg / $tot * 100;
$SER = $ser / $tot * 100;
$THR = $thr / $tot * 100;
$VAL = $val / $tot * 100;
$TRP = $trp / $tot * 100;
$TYR = $tyr / $tot * 100;



$triplets_spaced = join( " " ,@triplets);
$file = "Protein";

#Das ganze wird auf das File Protein geschrieben
open(PROTEINFILE , ">$file");

print PROTEINFILE "$triplets_spaced\n\n";

printf PROTEINFILE "Ala = %1.2f%\n\n", $ALA;
printf PROTEINFILE "Cys = %1.2f%\n\n", $CYS;
printf PROTEINFILE "Asp = %1.2f%\n\n", $ASP;
printf PROTEINFILE "Glu = %1.2f%\n\n", $GLU;
printf PROTEINFILE "Phe = %1.2f%\n\n", $PHE;
printf PROTEINFILE "Gly = %1.2f%\n\n", $GLY;
printf PROTEINFILE "His = %1.2f%\n\n", $HIS;
printf PROTEINFILE "Ile = %1.2f%\n\n", $ILE;
printf PROTEINFILE "Lys = %1.2f%\n\n", $LYS;
printf PROTEINFILE "Leu = %1.2f%\n\n", $LEU;
printf PROTEINFILE "Met = %1.2f%\n\n", $MET;
printf PROTEINFILE "Asn = %1.2f%\n\n", $ASN;
printf PROTEINFILE "Pro = %1.2f%\n\n", $PRO;
printf PROTEINFILE "Gln = %1.2f%\n\n", $GLN;
printf PROTEINFILE "Arg = %1.2f%\n\n", $ARg;
printf PROTEINFILE "Ser = %1.2f%\n\n", $SER;
printf PROTEINFILE "Thr = %1.2f%\n\n", $THR;
printf PROTEINFILE "Val = %1.2f%\n\n", $VAL;
printf PROTEINFILE "Trp = %1.2f%\n\n", $TRP;
printf PROTEINFILE "Tyr = %1.2f%\n\n", $TYR;


close PROTEINFILE;

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


exit;