perl应用：从基因组里分割染色体序列

染色体的结构：

>Chr1

nnnnnnnnnnnnnnnnnnnnnnnnnnnn

>Chr2

ATGCATGC

下面是程序：

use strict;
use warnings;

my $dna_filename;
my $DNA0='';
my $DNA1='';
my $DNA2='';
my $DNA3='';
my $DNA4='';
my $DNA5='';

print "please input the path just like this f:\perl\data.txtn";
chomp($dna_filename=<STDIN>);
open(DNAFILENAME,$dna_filename)||die("can not open the file!");

$/=">";

$DNA0=<DNAFILENAME>;
open (DNA0,">d:19DNA0.txt");
print DNA0 $DNA0;
close (DNA0);

$DNA1=<DNAFILENAME>;
open (DNA1,">d:19DNA1.txt");
print DNA1 ">".$DNA1;
close (DNA1);

$DNA2=<DNAFILENAME>;
open (DNA2,">d:19DNA2.txt");
print DNA2 ">".$DNA2;
close (DNA2);

$DNA3=<DNAFILENAME>;
open (DNA3,">d:19DNA3.txt");
print DNA3 ">".$DNA3;
close (DNA3);

$DNA4=<DNAFILENAME>;
open (DNA4,">d:19DNA4.txt");
print DNA4 ">".$DNA4;
close (DNA4);

$DNA5=<DNAFILENAME>;
open (DNA5,">d:19DNA5.txt");
print DNA5 ">".$DNA5;
close (DNA5);

2013年2月23日更新

上面的程序显然非常的麻烦，现在又重新用到了这个程序，所以进行了了简单的修改，程序在linux下运行：

#!/usr/bin/env perl 

use strict;
use warnings;
use utf8;

my $i;
my $DNA;
open(IN,"IRGSP-1.0_genome.fasta")||die("can not open");
$/=">";

for($i=0;$i<13;$i++)
{
    $DNA=<IN>;
    open(OUT,">chr$i")||die("can not open");
    print OUT ">$DNA";
    close OUT;
}

最近闲着没事有修改了一下：2013-07-16

这里的i是染色体条数+1；

use strict;  
use warnings;  
use utf8;  
  
open(IN,"a.txt")||die("can not open");  
$/=">";  
  
for(my $i=0;$i<5;$i++)  
{  
    my $DNA=<IN>;  
	$DNA=~m/(.+)/;
	my $name=$1;
    open(OUT,">$name.txt")||die("can not open");  
	$DNA=~m/(.+)>/s;
	my $result=$1;
    print OUT ">$result";  
    close OUT;  
}