2. Make a Perl program translating 'all' combinations of triple bases into amino acids -YJ code:309ir

aim . translating triple base codes convert into amino acids

 

 

 

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#!/usr/bin/perl
use strict;
use warnings;

1. this function is translating 'all' combinations of triple bases into amino acids
   

my %basetoaa= (
   "UUU" => "F", "UUC" => "F",
   "UUA" => "L", "UUG" => "L",
   "CUU" => "L", "CUC" => "L",
   "CUA" => "L", "CUG" => "L",
   "AUU" => "I", "AUC" => "I",
   "AUA" => "I", "AUG" => "M",
   "GUU" => "V", "GUC" => "V",
   "GUA" => "V", "GUG" => "V",
   
   "UCU" => "S", "UCC" => "S",
   "UCA" => "S", "UCG" => "S",
   "CCU" => "P", "CCC" => "P",
   "CCA" => "P", "CCG" => "P",
   "ACU" => "T", "ACC" => "T",
   "ACA" => "T", "ACG" => "T",
   "GCU" => "A", "GCC" => "A",
   "GCA" => "A", "GCG" => "A",
   
   "UAU" => "Y", "UAC" => "Y",
   "UAA" => "*", "UAG" => "*",
   "CAU" => "H", "CAC" => "H",
   "CAA" => "Q", "CAG" => "Q",
   "AAU" => "N", "AAC" => "N",
   "AAA" => "K", "AAG" => "K",
   "GAU" => "D", "GAC" => "D",
   "GAA" => "E", "GAG" => "E",
   
   "UGU" => "C", "UGC" => "C",
   "UGA" => "*", "UGG" => "W",
   "CGU" => "R", "CGC" => "R",
   "CGA" => "R", "CGG" => "R",
   "AGU" => "S", "AGC" => "S",
   "AGA" => "R", "AGG" => "R",
   "GGU" => "G", "GGC" => "G",
   "GGA" => "G", "GGG" => "G",
   
   "TTT" => "F", "TTC" => "F",
   "TTA" => "L", "TTG" => "L",
   "CTT" => "L", "CTC" => "L",
   "CTA" => "L", "CTG" => "L",
   "ATT" => "I", "ATC" => "I",
   "ATA" => "I", "ATG" => "M",
   "GTT" => "V", "GTC" => "V",
   "GTA" => "V", "GTG" => "V",
   
   "TCT" => "S", "TCC" => "S",
   "TCA" => "S", "TCG" => "S",
   "CCT" => "P", "CCC" => "P",
   "CCA" => "P", "CCG" => "P",
   "ACT" => "T", "ACC" => "T",
   "ACA" => "T", "ACG" => "T",
   "GCT" => "A", "GCC" => "A",
   "GCA" => "A", "GCG" => "A",
   
   "TAT" => "Y", "TAC" => "Y",
   "TAA" => "*", "TAG" => "*",
   "CAT" => "H", "CAC" => "H",
   "CAA" => "Q", "CAG" => "Q",
   "AAT" => "N", "AAC" => "N",
   "AAA" => "K", "AAG" => "K",
   "GAT" => "D", "GAC" => "D",
   "GAA" => "E", "GAG" => "E",
   
   "TGT" => "C", "TGC" => "C",
   "TGA" => "*", "TGG" => "W",
   "CGT" => "R", "CGC" => "R",
   "CGA" => "R", "CGG" => "R",
   "AGT" => "S", "AGC" => "S",
   "AGA" => "R", "AGG" => "R",
   "GGT" => "G", "GGC" => "G",
   "GGA" => "G", "GGG" => "G",
   "KYJ" => "error"
);
print "Guru : ";
print $basetoaa{"AAA"}; # K
print $basetoaa{"AUU"}; # I
print $basetoaa{"AUG"},"\n"; # M

## 변수입력
my $codon_data;
my $codon_data_length;
my @codon_data_split;
my @three_codon_data;
my @amino_acid_data;
my $amino_acid_length;
my $yorn1, $yorn2, $yorn3, $yorn4, $yorn5;
my $filename;

## Asking the way of how to input user's data(base).
print "This is a converting programm.\n\n";
print "Do you want to input your data using keyboard? [y/n] ";

1. input your choose in yorn.
   

$yorn1 = <STDIN>;

1. delete last enter key command 
   

chomp $yorn1;

1. print $yorn," \n";
   
2. yes -> using keyboard\ no-> using file\ else-> error\
   

if($yorn1 eq "y")
{
 print "<You want to input your data by using keyboard>\n";
}
elsif($yorn1 eq "n")
{
 print "<You want to input your data by using file>\n";
}
else
{
 print "<Error!>\n<you must input 'y' or 'n'.>\n";
 exit;
}

#--------------------------------------------------------------------

1. 1. input by keyboard
      

if ($yorn1 eq "y")
{
 ## input data 
 print "<please input your data using keyboard>\n"; #input data in $condon_data
 $codon_data = <STDIN>;
 chomp $codon_data;
 #delete (enter) command. chomp funtion delete last command.
 #because STDIN function memory all of command.
 #if do not use chomp, $codon_data is (Yeong Jae Kim 02:02, 27 May 2016 (KST))+(enter key)
 #so you must do it    
} 

## input through file.
elsif($yorn1 eq "n")
{
 print "---------------------------------------\n<Caution!>\n<You must put on your file in same directory>\n";
 print "<Do not write any word without codon data>\n";
 print "<Please input your file name without filename extension>\n";
 print "<If you want to input BRCA1.txt, just type BRCA1>\n---------------------------------\n";
 print "<Your input file name : ";
 $filename = <STDIN>;
 chomp $filename;
 # $filename = "$filename";
 open(TEXT, "$filename.txt");
 $codon_data = <TEXT>;
 close (TEXT);
 ## convert uppercase(대문자)-uc()
 $codon_data = uc($codon_data);
 # print $codon_data,"\n"; 
}

1. ------------------------------------------------------------------------

## confirm data
print "\nIs it yours?\n-----------------------------------\n$codon_data\n----------------------------------\n";
 

1. 1. convert uppercase(대문자)-uc()
      

$codon_data = uc($codon_data);
  

1. 1. check data length
      

$codon_data_length = length ($codon_data);
print "Codon length is $codon_data_length.\n";

1. if codon length is not multiply by 3, i notice warning message
   
2. print $codon_data_length%3;

## warning to data_length
if ($codon_data_length%3 ne "0")
{
 print "[warning] your codon length is not multiply by 3."; 
 print "Do you want continue? [y/n] ";
 $yorn2 = <STDIN>;
 chomp $yorn2; 
 if ($yorn2 eq "n")
 {
  exit; # just stop;
 }
}
 
 ## split codon_data
@codon_data_split = split(//, $codon_data);

1. print @codon_data;
   
2. print $codon_data[0];
   
3. print $codon_data[1];
   
4. print $codon_data[3];
   
5. print @codon_data_split,"\n";
   
6. my $i =3;
   
7. print $codon_data_split[$i];
   

 
 ## check data
foreach my $i (0..$#codon_data_split)
{
 ## U,T,C,A,G check
 if ($codon_data_split[$i] eq "U" || 
 $codon_data_split[$i] eq "T" || 
 $codon_data_split[$i] eq "C"|| 
 $codon_data_split[$i] eq "A"|| 
 $codon_data_split[$i] eq "G")
 {
  next;
 }
 else
 {
  print "[error]you do not input codon. please check your data\n";
  exit; 
 }
}
 ## divided 3 codons
for(my $i=0; $i < ($codon_data_length); $i=$i+3) 
{
 # print "this ($i/3) step";
 my $j=$i/3;
 $three_codon_data[$j] = $codon_data_split[$i].$codon_data_split[$i+1].$codon_data_split[$i+2];
 # print $three_codon_data[$j],"\n";
 # print length @three_codon_data;
 # you can't get size of array using length function
}
 # you just do to define scalar variable which equal array variable
 $amino_acid_length = @three_codon_data;
 # print "test1 = ",$amino_acid_length;
 # print @three_codon_data;
 # print $amino_acid_length;

 ## convert codon bases into amino acids
for (my $i=0; $i < ($amino_acid_length); $i++)
{
 # print $three_codon_data[$i];
 $amino_acid_data[$i] = $basetoaa{"$three_codon_data[$i]"};
 # print $amino_acid_data[$i],"\n";
} 

#-------------------------------------------------
 ## result
print "result : ",@amino_acid_data,"\n";

 ## alignment
print "<Do you want alignment?> [y/n] ";
$yorn3 = <STDIN>;
chomp $yorn3;
print "<Do you want see the number?> [y/n] ";
$yorn4 = <STDIN>;
chomp $yorn4;
if ($yorn3 eq "y")
{
 my $line = int($amino_acid_length/10);
 for (my $i=0; $i <= $line; $i++)
 {
    ## print number
   if ($yorn4 eq "y")
   {
    my $j =10*$i+1;
    print $j;   
    print "\n     ";
   } 
    ## print codon data
   for (my $j=0; $j < 10; $j++)
   {
    print $three_codon_data[10*$i+$j]," ";
   }  
   print "\n     ";
    ## print amino acid data
   for (my $j=0; $j < 10; $j++)
   {
    my $k = 10*$i+$j+1;
    if ($k == $amino_acid_length && $yorn2 eq "y")
    {
     print " ?", "\n";
    }
    else
    {
     print " ", $amino_acid_data[10*$i+$j], "  ";
    }  
   }
    print "\n";
  }
}

1. ----------------------------------------------------
   

 ## make result file
 print "<Do you want make file?> [y/n] ";
$yorn5 = <STDIN>;
chomp $yorn5;
 if ($yorn5 eq "y")
 {
  print "<What is the file name?>\n";
  print "<if you want to input BRCA1.txt, just type BRCA1>\n---------------------------------\n";
  print "<Your output file name : ";
  $output_filename = <STDIN>;
  chomp $output_filename;
  while ($filename eq $output_filename)
  {
   print "<This name is same to codon data file name.>\n";
   print "<Please input another name!!!> \n";
   print "<Your output file name : ";
   $output_filename = <STDIN>;
   chomp $output_filename;
  }
  # $output_filename = "$output_filename.txt";
  open (TEXT, ">$output_filename.txt"); 
  my $outputdata = join ("", @amino_acid_data);
  # print @amino_acid_data,"\n";
  # print $outputdata;
  print TEXT $outputdata;
  close (TEXT);
  print "Success! check your file";
  exit;
 }
 else 
 {
  exit;
 }