perl应用：六框阅读翻译DNA序列
生物学知识：
1.六框翻译
因为DNA为双链, 平时从NCBI等里面得到的只是其中的一条链,还有一个互补链没有结出. 先从一条链讲起, 如此链为ACGATGCCG....则现在有以下三种读法：第一种，ACG/ATG/CCG.... 第二种，把A看做前面的部分，则为A/CGA/TGC/CG..... 第三种，把AC看做是前面的部分，则为AC/GAT/GCC/G... 只此一条链就有三种读码框。当然，互补链也有其对应的三个读码框，所以两者加起来是六个读码框了。
比如序列：ACGACGACGACGACGACG，可能的读码框就有以下三种:
ACG ACG ACG ACG ACG ACG ACG ACG
CGA CGA CGA CGA CGA CGA CGA CGA
GAC GAC GAC GAC GAC GAC GAC GAC
use strict;
use warnings;
my $dna ='';
my $protein ='';
my @file_data=( );
my @filedata;
my $revcom='';
#打开文件
@filedata = get_file_data();
#得到序列
$dna = extract_sequence_from_fasta_data(@filedata);
#六框阅读翻译
print "\n---------------------Reading Frame 1-----------------\n";
$protein=translate_frame($dna,1);
print_sequence($protein,70);
print "\n---------------------Reading Frame 2-----------------\n";
$protein=translate_frame($dna,2);
print_sequence($protein,70);
print "\n---------------------Reading Frame 3-----------------\n";
$protein=translate_frame($dna,3);
print_sequence($protein,70);
print "\n---------------------Reading Frame 4-----------------\n";
$protein=translate_frame($dna,4);
print_sequence($protein,70);
print "\n---------------------Reading Frame 5-----------------\n";
$protein=translate_frame($dna,5);
print_sequence($protein,70);
print "\n---------------------Reading Frame 6-----------------\n";
$protein=translate_frame($dna,6);
print_sequence($protein,70);
sub get_file_data
{
# A subroutine to get data from a file given its filename
#读取文件的子序列
my $dna_filename;
my @filedata;
print "please input the Path just like this f:\\\\perl\\\\data.txt\n";
chomp($dna_filename=<STDIN>);
open(DNAFILENAME,$dna_filename)||die("can not open the file!");
@filedata = <DNAFILENAME>;
close DNAFILENAME;
return @filedata;#子函数的返回值一定要记住写
}
sub extract_sequence_from_fasta_data
{
#*******************************************************************
# A subroutine to extract FASTA sequence data from an array
# 得到其中的序列
# fasta格式介绍：
# 包括三个部分
# 1.第一行中以>开头的注释行，后面是名称和序列的来源
# 2.标准单字母符号的序列
# 3.*表示结尾
#*******************************************************************
my (@fasta_file_data) =@_;
my $sequence =' ';
foreach my $line (@fasta_file_data)
{
#这里忽略空白行
if ($line=~/^\s*$/)
{
next;
}
#忽略注释行
elsif($line=~/^\s*#/)
{
next;
}
#忽略fasta的第一行
elsif($line=~/^>/)
{
next;
}
else
{
$sequence .=$line;
}
}
$sequence=~s/\s//g;
return $sequence;
}
sub print_sequence
{
# A subroutine to format and print sequence data
my ($sequence, $length) = @_;
for (my $pos =0; $pos<length($sequence);$pos+=$length)
{
print substr($sequence,$pos,$length),"\n";
}
}
sub codon2aa
{
#第三种方法
#也就是运用哈希
#我们将所有的密码子作为hash的key，然后将代表的氨基酸作为hash的value
#然后进行匹配
# codon2aa
# A subroutine to translate a DNA 3-character codon to an amino acid
# Version 3, using hash lookup
my($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 \"$codon\"!!\n";
exit;
}
}
sub dna2peptide
{
my ($dna)=@_;
my $protein ='';
for (my $i=0; $i<(length($dna)-2);$i+=3)
{
$protein .=codon2aa(substr($dna,$i,3));
}
return $protein;#这个词错误找了一晚上，没有返回值，所以结果总是没有内容，以后要引以为戒，子程序一定要有返回值
}
sub translate_frame
{
my ($seq,$start,$end)=@_;
my $protein;
unless($end)
{
$end=length($seq);
}
return dna2peptide(substr($seq,$start-1,$end-$start+1));
}