my $previous_line; while (<$in>) { $current_line = $_; chomp $current_line; if(!defined($previous_line) || $. mod 2 != 0){ $previous_line = $current_line; next; } my @previous_columns = split(" ", $previous_line); my $end_coor = $previous_columns[2] + $previous_columns[3]; my @current_columns = split(" ", $current_line); my $seq_length = length $previous_columns[6]; my $gap_count = $previous_columns[6] =~ tr/Q//; my $original_length = $seq_length - $gap_count; my $original_end_coor = $previous_columns[2] + $original_length; my $distance = $current_columns[2] - $original_end_coor; $current_columns[2] = $end_coor + $distance; $previous_line = $current_line; print $out "$current_columns[2]\n"; } close $in; close $out;