#!/usr/bin/perl -w
use strict;

use Algorithm::Diff qw(traverse_sequences);

# construct arrayrefs containing an array of single chars
my ($A, $B) = map [/(.)/sg], qw(
	ATGGAGTCGACGAATTTGAAGAAT
	xxxxxxATGGAGyxxxTCGAzxxxxCGAATTTGAAxxwGAAT
);

my $prev = '';
my @seq;

traverse_sequences(
	$A, $B,
	{
		MATCH => sub {
			my ($aidx, $bidx) = @_;
			if('=' ne $prev) {
				push @seq, '';
				$prev = '=';
			}
			$seq[-1] .= $A->[$aidx];
		},
		DISCARD_A => sub { die "Sequence in A is not fully contained in B" },
		DISCARD_B  => sub {
			my ($aidx, $bidx) = @_;
			if('!' ne $prev) {
				push @seq, '';
				$prev = '!';
			}
			$seq[-1] .= $B->[$bidx];
		},
	},
);

print "@seq\n";

__END__
xxxxxx ATGGAG yxxx TCGA zxxxx CGAATTTGAA xxw GAAT