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

15,652 bytes added, 02:02, 27 May 2016

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aim . translating triple base codes convert into amino acids

~~strategy.~~

~~code.~~

-------------------------------------------------------------------------------------------------------------------------------------

#!/usr/bin/perl

use strict;

use warnings;

#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] ";

# input your choose in yorn.

$yorn1 = <STDIN>;

# delete last enter key command

chomp $yorn1;

# print $yorn," \n";

# 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;

}

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

## 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 ([[User:Yeong Jae Kim|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";

}

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

## confirm data

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

## convert uppercase(대문자)-uc()

$codon_data = uc($codon_data);

## check data length

$codon_data_length = length ($codon_data);

print "Codon length is $codon_data_length.\n";

# if codon length is not multiply by 3, i notice warning message

# 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);

# print @codon_data;

# print $codon_data[0];

# print $codon_data[1];

# print $codon_data[3];

# print @codon_data_split,"\n";

# my $i =3;

# 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";

}

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

## 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;

}

Anonymous user

imported>Yeong Jae Kim

Changes

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

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