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perl应用之SNP的提取（4）：信息的补全和重复区域的删除

发布时间：2020-09-07编辑：脚本学堂
在上一篇文章中，我们看了最后的输出结果如下：pos TAIR bur can ct edi hi kn ler mt no oy po rsch sf tsu wil ws wu zu

在上一篇文章中，我们看了最后的输出结果如下：
pos TAIR bur can ct edi hi kn ler mt no oy po rsch sf tsu wil ws wu zu  
1000 G - A - - - - - - - - - - - - - - - - 
10000003 C - - - - - G - - - - - - - - - - - - 
10000013 A - - R - - - - - - - - - - - - - - - 
10000021 G - - - - - - - - - - - C - - - - - - 
10000034 C - - - - - - - - - - - - - - - - Y - 
10000047 G R - - - - - - - - - - - - - - - R - 
10000049 A R - - - - - - - - - - - - - - - R - 

我们发现里面有许多的--当然详细看过上面文章的会知道，有些地方在一个sample是有SNP的。但是在另一个sample这个位置就可能不是一个SNP，这样，在这个位置就是一个空白。我们设置的输出就是-；

但是这一部分信息，也是我们需要的，所以我们要到原来的.maf文件中去回对，也就是把每个位置的每个样品的碱基信息进行统计。其实关键就是一个回对的过程。

所以我们的解决思路就是：
1.用合并后的信息，建立一个hash，方便后面的查找
2.打开.maf以后，我们对每一个块，（这里说的块，包括score部分，ref序列，sample序列），我们先看在ref中是否有这个点的信息，因为，我设置的score的起始位点是90000.所以会有很多无法匹配的位点。如果有，那么取sample中对应位置的碱基，保存到hash中。
3.重复回对每一个文件，最终得到最后的结果。
 

复制代码 代码如下:

#!/usr/bin/perl 
 
use strict; 
use warnings; 
 
my  %position; 
my  @information1; 
my  @mout; 
my  @score; 
my  @info1; 
my  @info2; 
my  @sequen1; 
my  @sequen2; 
my  $cout1; 
my  $cout; 
my  @samples; 
my  $samples; 
my  $key1; 
my  $value; 
my  $z;
 
open (DNA,"Chr5_join.txt")||die("can not open");#这里有需要替换成不同的染色体信息 
while(<DNA>) 
{ 
@information1=split; 
$position{$information1[0]}{sample0}=$information1[1]; 
} 
 
open (DNA1,"TAIR_vs_bur.maf")||die("can not open"); 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$z=<DNA1>; 
$/="nn"; 
while(<DNA1>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless ($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample1}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
} 
} 
 
open (DNA2,"TAIR_vs_can.maf")||die("can not open"); 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$z=<DNA2>; 
$/="nn"; 
while(<DNA2>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless ($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample2}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
}
} 
} 
 
open (DNA3,"TAIR_vs_ct.maf")||die("can not open"); 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$z=<DNA3>; 
$/="nn"; 
while(<DNA3>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample3}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA4,"TAIR_vs_edi.maf")||die("can not open"); 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$z=<DNA4>; 
$/="nn"; 
while(<DNA4>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample4}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA5,"TAIR_vs_hi.maf")||die("can not open"); 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$z=<DNA5>; 
$/="nn"; 
while(<DNA5>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample5}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
} 
} 
 
open (DNA6,"TAIR_vs_kn.maf")||die("can not open"); 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$z=<DNA6>; 
$/="nn"; 
while(<DNA6>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample6}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA7,"TAIR_vs_ler.maf")||die("can not open"); 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$z=<DNA7>; 
$/="nn"; 
while(<DNA7>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample7}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA8,"TAIR_vs_mt.maf")||die("can not open"); 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$z=<DNA8>; 
$/="nn"; 
while(<DNA8>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample8}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA9,"TAIR_vs_no.maf")||die("can not open"); 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$z=<DNA9>; 
$/="nn"; 
while(<DNA9>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample9}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA10,"TAIR_vs_oy.maf")||die("can not open"); 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$z=<DNA10>; 
$/="nn"; 
while(<DNA10>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample10}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA11,"TAIR_vs_po.maf")||die("can not open"); 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$z=<DNA11>; 
$/="nn"; 
while(<DNA11>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample11}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA12,"TAIR_vs_rsch.maf")||die("can not open"); 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$z=<DNA12>; 
$/="nn"; 
while(<DNA12>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample12}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA13,"TAIR_vs_sf.maf")||die("can not open"); 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$z=<DNA13>; 
$/="nn"; 
while(<DNA13>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample13}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA14,"TAIR_vs_tsu.maf")||die("can not open"); 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$z=<DNA14>; 
$/="nn"; 
while(<DNA14>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample14}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA15,"TAIR_vs_wil.maf")||die("can not open"); 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$z=<DNA15>; 
$/="nn"; 
while(<DNA15>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample15}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA16,"TAIR_vs_ws.maf")||die("can not open"); 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$z=<DNA16>; 
$/="nn"; 
while(<DNA16>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample16}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA17,"TAIR_vs_wu.maf")||die("can not open"); 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$z=<DNA17>; 
$/="nn"; 
while(<DNA17>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample17}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
open (DNA18,"TAIR_vs_zu.maf")||die("can not open"); 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$z=<DNA18>; 
$/="nn"; 
while(<DNA18>) 
{ 
@mout = split/n/,$_; 
@score= split/=/, $mout[0]; 
unless($score[1]<90000) 
{ 
@info1 = split/s+/,$mout[1]; 
@info2 = split/s+/,$mout[2]; 
 
@sequen1 = split// ,$info1[6]; 
@sequen2 = split// ,$info2[6]; 
 
for($cout1=$info1[2]+1;$cout1<$info1[3]+$info1[2]+1;$cout1++) 
{ 
if(exists $position{$cout1}) 
{ 
$cout=$cout1-$info1[2]-1; 
$position{$cout1}{sample18}=$sequen2[$cout]; 
} 
else  
{ 
next; 
} 
} 
 
} 
} 
 
@samples=qw/sample0 sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18/; 
 
open(ALL,">all_information.txt")||die("can not open!"); 
 
foreach $key1(sort keys %position) 
{ 
print ALL "$key1 "; 
foreach $samples(@samples) 
{ 
if(exists $position{$key1}{$samples}) 
{ 
$value = $position{$key1}{$samples}; 
print ALL "$value "; 
} 
else 
{ 
print ALL "- " 
} 
} 
print ALL "n"; 
} 


结果如下：
10001656 G G - - G - G G G G - G A G G A G G G  
10001667 G G - - G - G G G G - G G G G S G G G  
10001670 G G - - G T G G G G - G G G G G G G G  
10001672 T T - - T G T T T T - T T T T T T T T  
10001673 G G - - G A G G G G - G G G G G G G G  
10001696 G G - - G G G G G G - G A G G A G G G  
10001713 C C - - C C C C C C - C C C C Y C C C  
10001768 C C - - C C C C C C - C C C C Y C C C  
10001791 A A - - G G G G A A - A G A G G A A G  
10001812 G G - - G G G G A A - G G G G G G G G  
10001816 A A - - A A A A A A - A G A A G A A A  
10001820 C C - - C C C C C C - C C C C S C C C  

我们可以看到好多位置的信息已经补充完整了。

然后一个新的问题就是，我们知道基因在测序的过程中会有很多的重复区域，我们也要把相应的重复区域删除。
删除重复区域其实也是一个hash应用的过程。没有多少亮点。

我们首先来看一下这个repeat区域的格式：
5   0   4758 
5   52485289 
5   56677   56887 
5   63698   63796 
5   64015   64047 
5   64771   71199 
5   78471   78531 
5   138655  138720 
5   138941  139927 
5   140759  140948 
5   162806  162844 
5   301999  302104 

我们要做的就是确定第一个，和最后一个位置，然后利用if循环，使数据递增。然后检查hash中时候有这样一个key值的存在，如果有的话，那么就delete这个hash，如果没有的就保存。就是这样。

我们来看一下代码：
#!/usr/bin/perl 
# move repeat arear out 
 
use strict; 
use warnings; 
 
my %position; 
my @pos; 
my $cout; 
my $key; 
my $value; 
 
open (ALL,"all_information.txt")||die("can not open!"); 
while(<ALL>) 
{ 
$position{$1}=$2 if $_=~/^(d+)s(.+)$/; 
} 
 
open (POS,"sepChr5.txt")||die("can not open!"); 
while(<POS>) 
{ 
@pos=split; 
for($cout=$pos[1]+1;$cout<$pos[2]+1;$cout++) 
{ 
if(exists $position{$cout}) 
{ 
delete $position{$cout}; 
} 
else  
{ 
next; 
} 
} 
} 
 
open (RESULT,">without_repeat_information.txt")||die ("can not open!"); 
foreach $key(sort keys %position) 
{ 
print RESULT "$key "; 
$value=$position{$key}; 
print RESULT "$value n"; 
}

上一篇：perl应用之SNP的提取（3）：18个样品SNP的合并+忽略-多的行
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