The part causing troubles is: 
foreach my $id (@ids) {
       if ($id eq $NSC) {
           print MY $line;
       }
    }

[download]
and the uninitialized value is *** $id. ***.
Well. $id comes from @ids. Where does @ids come from?

You declare @ids about 20 ish lines above, and then populate the array with (reformatted, for clarity) 

foreach my $row (@ids_table) {
    my @allcolumns = split /\t/, $row;
    if($count==0) {
        $myID= trim($allcolumns[0]);
    }
    else {
        $ids[$count] = trim($allcolumns[0]);
    }
    $count++;
}

[download]

You perform different actions on your input when $count is zero, but you're still adding it to the array with $ids[$count] = ... inside the else block. So, $ids[0] is always going to be undefined.

If you want to add something to the end of an array, use push, not subscripts.

In reply to Re: Uninitialized value in string eq error but I initialized by FunkyMonk
in thread Uninitialized value in string eq error but I initialized by karpatov

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