#!/bin/perl
use warnings;
use strict;

open (file1,"6hrepCLIP.txt") or die "$!\n";
open (file1b,"6hrepb.txt") or die "$!\n";
open (file1c,"genetable_validsigdiffkovswt6h_strict.bed") or die "$!\n";
open (file2,">Tablesgenesmerged6h_1") or die "$!\n";
open (file2b,">Tablesgenesmerged6h_2") or die "$!\n";

my %matrix1;
my %matrix2;
my %matrix3;
my %matrix4;
my %matrix5;

my $temp1=0;
my $temp2=0;
my $temp3=0;
my $temp4=0;
my $temp5=0;

my $var1=0;
my $var2=0;
my $var3=0;

my $signal1=0;



while(my $line1=<file1>)  
 {   
     @{$matrix1{$temp1}}=split(/\s/,$line1);
   
     $temp1++;
 }

while(my $line1c=<file1c>)  
 {   
     @{$matrix2{$temp2}}=split(/\s/,$line1c);
   
     $temp2++;
 }

while(my $line1b=<file1b>)  
 {

@{$matrix3{$temp3}}=split(/\s/,$line1b);  

for ( my $i=0; $i<$temp1; $i++)
 {   
    if ( ( ${$matrix1{$i}}[9] eq ${$matrix3{$temp3}}[0] ) )
    { 
        if  (( ${$matrix1{$i}}[0] eq ${$matrix1{$i-1}}[0] )||( ${$matrix1{$i}}[1] eq ${$matrix1{$i-1}}[1] )||( ${$matrix1{$i}}[2] eq ${$matrix1{$i-1}}[2] ))
         {  }
print file2 "${$matrix1{$i}}[9]\t${$matrix1{$i}}[0]\t${$matrix1{$i}}[1]\t${$matrix1{$i}}[2]\t${$matrix1{$i}}[3]\t${$matrix1{$i}}[4]\t${$matrix1{$i}}[5]\n";
    
    }

}

####################################################################################
for ( my $j=0; $j<$temp2; $j++)
 {   
    if ( ( ${$matrix2{$j}}[2] eq ${$matrix3{$temp3}}[0] ) )
    { 
  
print file2b "${$matrix2{$j}}[0]\t${$matrix2{$j}}[1]\t${$matrix2{$j}}[2]\t${$matrix2{$j}}[3]\t${$matrix2{$j}}[4]\t${$matrix2{$j}}[5]\t${$matrix2{$j}}[6]\t${$matrix2{$j}}[7]\t${$matrix2{$j}}[8]\t${$matrix2{$j}}[9]\t${$matrix2{$j}}[10]\t${$matrix2{$j}}[11]\t${$matrix2{$j}}[12]\t${$matrix2{$j}}[13]\n";
    
    }

}

$temp3++;

}

 close (file2);