Hello, I have such problem: I want to print all lines with new added column: IN or OUT, the script runs, but I can't understand, why there is only first line printed...do you have any suggestions?

This is my script: 

use strict; 
use warnings; 


open(FILE, "Q.txt");
my $file = <FILE>;                  

my @column; 
while (<FILE>) {                          
@column=($file);

chomp @column;  

my $number=0;

    while($number <= $#column) {    #go through the array from 0 to th
+e last element 
    my $j;
     my $count=0;
     foreach ($j=$number; $j < $#column; $j++)  {  #select the numbers
+ from the beginning of the line  
     my $d=($column[$j]=~/(\d+)/)[0] - ($column[$j+1]=~/(\d+)/)[0]; #d
+ifference
            last if abs($d)!= 1;          #if differ more than 1 - lea
+ve. 


      $count+=$d;              #accumulate the difference.     


}     
    if(abs($count)>=8) {                        
    $column[$_].= " t\IN "     
 for $number..$j;                     
     $number=$j+1;                          
    }                        


    if(abs($count)<8){               
   $column[$number].= " \tOUT" ;                                
   $number++;        
    }      
}         
}        
print for @column;              
exit;

[download]

And here is my INPUT FILE: 

5 Q CAA   
16 Q CAG   
21 Q CAA  
74 Q CAA  
80 Q CAG  
82 Q CAG  
84 Q CAG   
85 Q CAG   
89 Q CAG  
90 Q CAG  
91 Q CAG  
92 Q CAG  
93 Q CAA  
94 Q CAG  
95 Q CAG  
96 Q CAG  
98 Q CAG  
99 Q CAG  
100 Q CAG  
101 Q CAG 
102 Q CAG  
106 Q CAG  
107 Q CAG

[download]

Here is my OUTPUT FILE, but here is just the 1st line...:

5 Q CAA OUT

[download]

Thank you!

2017-08-12 Athanasius added code tags around data

In reply to How can I print all lines? by 345qwerty

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