#!/usr/bin/env perl use strict; use warnings; my %seen; $/=""; while (<>) { chomp; my ( $key, $value ) = split('\t', $_); my @lines = split /\n/, $key; my $key1 = $lines[1]; push( @{ $seen{$key1} }, $value ); } foreach my $key1 ( sort keys %seen ) { print join( "\t", $key, @{ $seen{$key1} } ); }