#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my ($ref_file, $data_file) = qw{pm_1146340_file1.txt pm_1146340_file2.txt};
my (%ref_left, %ref_right, @output);

open my $ref_fh, '<', $ref_file;
while (<$ref_fh>) {
    chomp;
    undef $ref_left{$_};
}
close $ref_fh;

open my $data_fh, '<', $data_file;
while (<$data_fh>) {
    my ($left, $right) = split ' ', $_, 2;
    next unless exists $ref_left{$left} and not defined $ref_left{$left};
    ++$ref_left{$left};
    ++$ref_right{$right};
}
seek $data_fh, 0, 0;
while (<$data_fh>) {
    my ($left, $right) = split ' ', $_, 2;
    next unless $ref_right{$right}; 
    push @output, $_;
}   
close $data_fh;

print for @output;

##</code><code>##

123 string 1
111 string 1
222 string 1
333 string 1
456 string 2
444 string 2
555 string 2
666 string 2
789 string 3
777 string 3
888 string 3
999 string 3

##</code><code>##

123 string 1
111 string 1

##</code><code>##

111 string 1
123 string 1

##</code><code>##

123 string 4
111 string 4

##</code><code>##

while (<$ref_fh>) {
    chomp;
    ++$ref_left{$_};
}
...
while (<$data_fh>) {
    my ($left, $right) = split ' ', $_, 2;
    next unless $ref_left{$left} or $ref_right{$right};
    ++$ref_right{$right};
}