G'day filipo,

I see ++toolic has pointed out issues in you code. Here's my take on a solution (pm_graph_undirected.pl) which uses glob to generate the combinations.

#!/usr/bin/env perl -l

use strict;
use warnings;
use autodie;

use Graph::Undirected;

my $graph = Graph::Undirected::->new();

open my $input_fh, '<', './pm_graph_undirected.txt';

while (<$input_fh>) {
    my ($x, $y) = /^\w+[#]([^<]+)\s+<=>\s+(.*)$/;
    
    $graph = $graph->add_edge(split /,/) for glob join ',' =>
        map { '{' . join(',' => split /[+ ]+/ => $_) . '}' } ($x, $y);
}   

print $graph;
[download]

Input:

$ cat pm_graph_undirected.txt
R1#C01+ C02 <=> C03 + C04
R2#C01 + C04 + C05 <=> C07 + C08 + C09
[download]

Output:

$ pm_graph_undirected.pl
C01=C03,C01=C04,C01=C07,C01=C08,C01=C09,C02=C03,C02=C04,C04=C07,C04=C0
+8,C04=C09,C05=C07,C05=C08,C05=C09
[download]

Update: ++choroba has pointed out a limitation with glob (below). I've tracked down details: see GLOB_LIMIT in File::Glob - POSIX FLAGS.

[Update2: very minor code change to remove an unnecessary comma s['}',]['}'] in the map. Retested and got the same output.]