G'day 345qwerty,

"Do you have any suggestions?"

If you write code that messy, you can be pretty much guaranteed to make mistakes. Choose a code layout that suits you and use it consistently. See "perlstyle - Perl style guide" for tips on how to accomplish this. Consider using "perltidy - a perl script indenter and reformatter".

open(FILE, "<", "Q.txt");
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Use lexical filehandles instead of global, package variables. Check that I/O operations actually worked. See open and the autodie pragma.

        while($number <= $#column) {       #go through the array from 
+0 to the last element
                   $number++;
                 }
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This is an inappropriate method for iterating an array. If you just want the elements:

for my $element (@array_name) {
    # Do something with $element here
}
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If you really need the indexes:

for my $index (0 .. $#array_name) {
    # Do something with $index here
}
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I might have further suggestions after you've tidied up the code.