R1.txt @NS500278:42:HC7M3AFXX:3:21604:26458:18476 2:N:0:AGTGGTCA AAAAAAAAACAGATATTTGCACTAGGCATTATAAATAACATCAATTAAGTAAAAAAATTA + AAAAAEEEEAEEEEEEEEEE/AEEEEEEEEEEEE 1:R1.txt #### R2.txt @NS500278:42:HC7M3AFXX:3:21604:26458:18476 2:N:0:AGTGGTCA AAAAAAAAACAGATATTTGCACTAGGCATTATAAATAACATCAATTAAGTAAAAAAATTA + AAAAAEEEEAEEEEEEEEEE 1:R2.txt #### The output I want is: output @NS500278:42:HC7M3AFXX:3:21604:26458:18476 2:N:0:AGTGGTCA AAAAAAAAACAGATATTTGCACTAGGCATTATAAATAACATCAATTAAGTAAAAAAATTA + AAAAAEEEEAEEEEEEEEEE/AEEEEEEEEEEEE 1:R1.txt 1:R2.txt count:2 #### My code is: #!/usr/bin/env perl use strict; use warnings; no warnings qw( numeric ); my %seen; $/ = ""; while (<>) { chomp; my ($key, $value) = split ('\t', $_); my @lines = split /\n/, $key; my $key1 = $lines[1]; $seen{$key1} //= [ $key ]; push (@{$seen{$key1}}, $value); } foreach my $key1 ( sort keys %seen ) { my $tot = 0; my $file_count = @ARGV; for my $val ( @{$seen{$key1}} ) { $tot += ( split /:/, $val )[0]; } if ( @{ $seen{$key1} } >= $file_count) { print join( "\t", @{$seen{$key1}}); print "\tcount:". $tot."\n\n"; } }