#!/usr/bin/perl use warnings; use strict; while(<>){ my $hitlength; my $prevalence; my $prev_l; my $prev_p ; my $line = $_; chomp $line; if($line =~ /^[\d]/){ my @hitline = split(/,/ , $line); $hitlength = $hitline [4]; $prevalence = $hitline [65]; if($hitlength == $prev_l and $prevalence == $prev_l){ next; } else { print "$line\n"; } $prev_l=$hitlength; $prev_p=$prevalence; } }