Hello again 345qwerty,

What this is reply is suppose to be? It is easy to see that your code is not written by you, you copy pasted some parts and you hope that this work.

Your code is not compiling:

$ perl test.pl
Use of uninitialized value $file in scalar chomp at test.pl line 10.
[download]

After fixing your error and modifying your code to be able to compile, I get the following:

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

my $path2file = 'Q.txt';

open my $fh, '<', $path2file;
chomp(my @column = <$fh>);
close $fh;

my $number=0;
while($number <= $#column) { #go through the array from 0 to the last 
+element
    my $j;
    my $count=0;
    foreach ($j=$number; $j < $#column; $j++) { #select the numbers fr
+om the beginning of the line in the current and next element
    my $d=($column[$j]=~/(\d+)/)[0] - ($column[$j+1]=~/(\d+)/)[0]; #di
+fference
    last if abs($d)!= 1; #if differ more than 1 - leave
    $count+=$d; #accumulate the difference
    }
    if(abs($count)>=7) {
    chomp($column[$_]);
    $column[$_]=$column[$_]. "\tIN\n" for $number..$j; #IN if >8
    $number=$j+1;
    }
    if (abs($count)<8) {
    chomp($column[$number]);
    $column[$number] = $column[$number]."\tOUT\n"; #OUT if < 8
    $number++;
    }
}
print for @column;

__END__

$ perl test.pl
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
Use of uninitialized value in subtraction (-) at test.pl line 16.
5    Q    CAA    OUT
    OUT
16    Q    CAG    OUT
    OUT
21    Q    CAA    OUT
    OUT
74    Q    CAA    OUT
    OUT
80    Q    CAG    OUT
    OUT
82    Q    CAG    OUT
    OUT
84    Q    CAG    OUT
    OUT
85    Q    CAG    OUT
    OUT
89    Q    CAG    OUT
    OUT
90    Q    CAG    OUT
    OUT
91    Q    CAG    OUT
    OUT
92    Q    CAG    OUT
    OUT
93    Q    CAA    OUT
    OUT
94    Q    CAG    OUT
    OUT
95    Q    CAG    OUT
    OUT
96    Q    CAG    OUT
    OUT
98    Q    CAG    OUT
    OUT
99    Q    CAG    OUT
    OUT
100    Q    CAG    OUT
[download]

Make your code executable, make your code produce the output file and then I could spend some time to assist you. I am sorry at this point I stop. When someone spends his time for free trying to assist you and you simply copy paste a reply to a question into a non compiling code, sorry but there is not point of working on this anymore. Maybe another monk will be more patient to assist you.

Update your code and your attitude and then we can talk about it again, BR.

Well it is plainly obvious that you are leaving the \n on the IN lines, isnt it? Why dont you look at where you append IN to see what may be wrong?

Just what do you expect $_ to have in it when you say chomp($column[$_]);?