#!/usr/bin/perl
use strict;
use warnings;

my ($infile1, $infile2) = ('abc', 'def');
my ($outfile1, $outfile2, $outfile3) = ('out.both', 'out.1', 'out.2');

open my $IF1, "sort -k3 $infile1 |' or die "opening $infile1: $!";
open my $IF2, 'sort -k3 $infile2 |' or die "opening $infile2: $!";
open my $OF1, '>', $outfile1 or die "opening $file1: $!";
open my $OF1, '>', $outfile2 or die "opening $file2: $!";
open my $OF1, '>', $outfile3 or die "opening $file3: $!";

my $f1 = <$IF1>;
my $f2 = <$IF2>;

while (defined($f1) or defined($f2)) {
    if ($f1 eq $f2) {
        print $OF1 $f1;
        $f1 = <$IF1>;
        $f2 = <$IF2>;
    }
    elsif ($f1 lt $f2) {
        print $OF2 $f1;
        $f1 = <$IF1>;
    }
    else {
        print $OF3 $f2;
        $f2 = <$IF2>;
    }
}