Question

I have a script that utilizes a hash, which contains four strings as keys whose values are hashes. These hashes also contain four strings as keys which also have hashes as their values. This pattern continues up to n-1 levels, which is determined at run-time. The nth-level of hashes contain integer (as opposed to the usual hash-reference) values.

I installed the BerkeleyDB module for Perl so I can use disk space instead of RAM to store this hash. I assumed that I could simply tie the hash to a database, and it would work, so I added the following to my code:

my %tags = () ; 
my $file = "db_tags.db" ; 
unlink $file; 


tie %tags, "BerkeleyDB::Hash", 
        -Filename => $file, 
        -Flags => DB_CREATE
     or die "Cannot open $file\n" ;

However, I get the error:

Can’t use string (“HASH(0x1a69ad8)”) as a HASH ref while “strict refs” in use at getUniqSubTreeBDB.pl line 31, line 1.

To test, I created a new script, with the code (above) that tied to hash to a file. Then I added the following:

my $href = \%tags; 
$tags{'C'} = {} ;

And it ran fine. Then I added:

$tags{'C'}->{'G'} = {} ;

And it would give pretty much the same error. I am thinking that BerkeleyDB cannot handle the type of data structure I am creating. Maybe it was able to handle the first level (C->{}) in my test because it was just a regular key -> scaler?

Anyways, any suggestions or affirmations of my hypothesis would be appreciated.

Answer 1

Use DBM::Deep.

my $db = DBM::Deep->new( "foo.db" );

$db->{mykey} = "myvalue";
$db->{myhash} = {};
$db->{myhash}->{subkey} = "subvalue";

print $db->{myhash}->{subkey} . "\n";

The code I provided yesterday would work fine with this.

sub get_node {
   my $p = \shift;
   $p = \( ($$p)->{$_} ) for @_;
   return $p;
}

my @seqs = qw( CG CA TT CG );

my $tree = DBM::Deep->new("foo.db");
++${ get_node($tree, split //) } for @seqs;