#!/usr/bin/perl use strict; my (%hash, %hash_key); my $x = 0; while (){ my @array = split(' ', $_); $x++; $hash{"$array[1]-$array[4]"} = $_; $hash_key{$x} = "$array[1]-$array[4]"; } foreach my $i (sort {$a <=> $b} keys %hash_key){ (exists $hash{$hash_key{$i}}) ? (print "$hash{$hash_key{$i}}") : (print "deleted\n"); delete($hash{$hash_key{$i}}) if (exists $hash{$hash_key{$i}}); } __DATA__ A 83 GLU A 90 GLU A 163 ARG A 83 ARG A 222 ARG A 5 ARG A 229 ALA A 115 ALA A 257 ALA A 118 ALA A 328 ASP A 95 ASP A 83 GLU A 90 GLU A 163 ARG A 83 ARG A 222 ARG A 5 ARG A 83 GLU B 90 GLU A 163 ARG B 83 ARG A 222 ARG B 5 ARG