#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Carp;
use Algorithm::Combinatorics qw( combinations );
use Set::CrossProduct;

my $str1 = '[TA]TTCGG';
my $e  = 2;

find_nb($str1,$e);

sub find_nb {

    my ( $str, $d ) = @_;

    my @base = $str =~ /\G ( \[ [^][]+ \] | [^][] ) /xg;

    #my @base = split //, $str;

    for my $exact_distance ( 1 .. $d ) {
        my $change_idx_iter
            = combinations( [ 0 .. $#base ], $exact_distance );

        while ( my $change_idx = $change_idx_iter->next ) {
            my @base_combo = map {
                my $i = $_;

                [ grep { $base[$i] !~ $_ } qw( A T C G ) ];

                #[ grep { $base[$i] ne $_ } qw( A T C G ) ];
            } @$change_idx;

            push @base_combo, [0] if $exact_distance == 1;

            my $bases_iter = Set::CrossProduct->new( \@base_combo );

            my @neighbour = @base;

            while ( my $new_bases = $bases_iter->get ) {
                @neighbour[@$change_idx] = @$new_bases;

                #$_ = "[$_]" for @neighbour[@$change_idx];

                my $str = join( "", @neighbour );
                print "$str\n";

            }

        }
    }

    return;
}