Hi,

hopefully this helps to get your mind around your problem:

#!/usr/bin/perl
use strict;
use warnings;
use 5.010;

use Data::Dumper;

my %neigbours;

while (my $line = <DATA>) {
    chomp $line;
    my ($id_pathway, @pathnodes) = split ' ', $line;
    my $path_length = @pathnodes;
    if($path_length < 2) {
        warn "Don't know whether paths with less than two nodes are al
+lowed. Skipping.";
        next;
    }
    for (my $i = 0; $i < $path_length - 1; $i++) {
        my $key = "$pathnodes[$i]$pathnodes[$i+1]";
        if(defined $neigbours{$key}) {
            if($neigbours{$key}->{'minpathlen'} >= $path_length) {
                $neigbours{$key}->{'minpathlen'} = $path_length;
                $neigbours{$key}->{'id_pathway'} = $id_pathway;
            }
        }
        else {
            $neigbours{$key}->{'minpathlen'} = $path_length;
            $neigbours{$key}->{'id_pathway'} = $id_pathway;
        }
    }
}

say Dumper(\%neigbours);

__DATA__
A a b c d e f
B a b c
[download]

Allow me an annotation: Please use meaningful variable names. Your code is hard to read.

Regards
McA