Perl/make_CDS_to_Codon.pl at master · gaorongchao/Perl · GitHub

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use warnings;
use strict;
my $dna='cgacgtcttcgtacgggactagctcgtgtcggtcgc';
my $protein=' ';
my $codon;
=cut
for(my $i=0; $i<(length($dna)-2);$i+=3)
{
    $codon=substr($dna,$i,3);
    $protein.=codon2aa($codon);
}
print "I translated the DNA\n\n$dna\n\n into the protein\n\n$protein\n\n";
exit;
=cut

my	$out_out = "result.txt";
open  my $out, '>', $out_out or die  "failed open$!\n";

my	$in_in = "a&b_result.txt";
open  my $in, '<', $in_in or die "cannot open\n";
while(<$in>)
{
	chomp;
	my $line1=$_;
	my $dna=<$in>;
	chomp($dna);
	my $protein=' ';
	for (my $i=0;$i<(length($dna)-2);$i+=3)
	{
		my $codon=substr($dna,$i,3);
		my $a=codon2aa($codon);
		$protein="$protein"."$a";
	}
	print $out "$line1\n$protein\n";
}
close  $in;

close  $out;

#*****************************************************************************************8
# codon2aa
#
# A subroutine to translate a DNA 3-character codon to an amino acid
#   Version 3, using hash lookup

sub codon2aa
{
    my($codon) = @_;

    $codon = uc $codon;#uc=uppercase;lc=lowercase
                   #也就是大小写转换，uc表示将所有的小写 转换为大写
               #lc将所有的大写转换为小写

    my(%genetic_code) = (

    'TCA' => 'S',    # Serine
    'TCC' => 'S',    # Serine
    'TCG' => 'S',    # Serine
    'TCT' => 'S',    # Serine
    'TTC' => 'F',    # Phenylalanine
    'TTT' => 'F',    # Phenylalanine
    'TTA' => 'L',    # Leucine
    'TTG' => 'L',    # Leucine
    'TAC' => 'Y',    # Tyrosine
    'TAT' => 'Y',    # Tyrosine
    'TAA' => '_',    # Stop
    'TAG' => '_',    # Stop
    'TGC' => 'C',    # Cysteine
    'TGT' => 'C',    # Cysteine
    'TGA' => '_',    # Stop
    'TGG' => 'W',    # Tryptophan
    'CTA' => 'L',    # Leucine
    'CTC' => 'L',    # Leucine
    'CTG' => 'L',    # Leucine
    'CTT' => 'L',    # Leucine
    'CCA' => 'P',    # Proline
    'CCC' => 'P',    # Proline
    'CCG' => 'P',    # Proline
    'CCT' => 'P',    # Proline
    'CAC' => 'H',    # Histidine
    'CAT' => 'H',    # Histidine
    'CAA' => 'Q',    # Glutamine
    'CAG' => 'Q',    # Glutamine
    'CGA' => 'R',    # Arginine
    'CGC' => 'R',    # Arginine
    'CGG' => 'R',    # Arginine
    'CGT' => 'R',    # Arginine
    'ATA' => 'I',    # Isoleucine
    'ATC' => 'I',    # Isoleucine
    'ATT' => 'I',    # Isoleucine
    'ATG' => 'M',    # Methionine
    'ACA' => 'T',    # Threonine
    'ACC' => 'T',    # Threonine
    'ACG' => 'T',    # Threonine
    'ACT' => 'T',    # Threonine
    'AAC' => 'N',    # Asparagine
    'AAT' => 'N',    # Asparagine
    'AAA' => 'K',    # Lysine
    'AAG' => 'K',    # Lysine
    'AGC' => 'S',    # Serine
    'AGT' => 'S',    # Serine
    'AGA' => 'R',    # Arginine
    'AGG' => 'R',    # Arginine
    'GTA' => 'V',    # Valine
    'GTC' => 'V',    # Valine
    'GTG' => 'V',    # Valine
    'GTT' => 'V',    # Valine
    'GCA' => 'A',    # Alanine
    'GCC' => 'A',    # Alanine
    'GCG' => 'A',    # Alanine
    'GCT' => 'A',    # Alanine
    'GAC' => 'D',    # Aspartic Acid
    'GAT' => 'D',    # Aspartic Acid
    'GAA' => 'E',    # Glutamic Acid
    'GAG' => 'E',    # Glutamic Acid
    'GGA' => 'G',    # Glycine
    'GGC' => 'G',    # Glycine
    'GGG' => 'G',    # Glycine
    'GGT' => 'G',    # Glycine
    );

    if(exists $genetic_code{$codon})
    {
        return $genetic_code{$codon};
    }
    else
    {

            print STDERR "Bad codon \"$codon\"!!\n";
            exit;
    }
}

#*****************************************************************************************