IUPAC nucleotide code から uniq sequence を取得

例えば、AAARCCCWTTTNGGG とかって IUPAC 配列があり、 R, W, N を [ACGT] に変換した全ての配列が欲しくなった場合。

普通に書く

my %nbc = (
    M => [ qw( A C ) ],
    R => [ qw( A G ) ],
    W => [ qw( A T ) ],
    S => [ qw( C G ) ],
    Y => [ qw( C T ) ],
    K => [ qw( G T ) ],
    V => [ qw( A C G ) ],
    H => [ qw( A C T ) ],
    D => [ qw( A G T ) ],
    B => [ qw( C G T ) ],
    N => [ qw( A C G T ) ],
    A => [ qw( A ) ],
    C => [ qw( C ) ],
    G => [ qw( G ) ],
    T => [ qw( T ) ],
) ;

my $str = q{AAARCCCWTTTNGGG} ;
my @ret = ( q{} ) ;
for my $s ( split //, uc $str ){
    @ret = map { my $r = $_ ; map{ $r . $_ } @{$nbc{$s}} } @ret 
}

printf "%s\n", $_ for @ret ;

Bio::Tools::IUPAC

BioPerl の これ の例文ほぼそのまんま。

use Bio::PrimarySeq;
use Bio::Tools::IUPAC;

my $ambiseq = Bio::PrimarySeq->new(-seq => 'AAARCCCWTTTNGGG', -alphabet => 'dna');
my $iupac = Bio::Tools::IUPAC->new(-seq => $ambiseq);
while (my $uniqueseq = $iupac->next_seq()) {
    print $uniqueseq->seq . "\n" ; 
}