use warnings; use strict; open (IN, "in.txt") or die; open (OUT, "out.txt") or die; my $previous_line = ; while (my $current_line = ) { chomp $current_line; chomp $previous_line; 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;