Hi everyone, I'am searching for a fast and convenient way to store and retrieve biological data from large data files (>2GB) but
I can't use any RDBMS etc, just flat files.
First I stored the complete file in XML format. To fetch particular datasets I had to read in the file completely (in worst case).

Then I read about DB_File/BerkeleyDB and figured that it might be useful. I tried it with a smaller description file (~50MB)
and everything seemed to work quite nice and search time was significantly improved.
But then I tried one of the bigger files (1.2GB) and had to stop my script after 15 minutes because the resulting database file
was already >6GB!

My questions are:
1. Is it my code that's going wrong for large files(see code below)?
OR
2. Is it a typical behavior of File_DB and huge datafiles, i.e. normal that the output file is more than 6 times bigger than the datafile?
AND IF SO
3. Is there a better solution? (I read something about File::Tie instead of DB_File tie...)


I appreciate any help.

Cheers,
Lowry 
# Takes the output directory name $annotationDirName
# and a hash-ref of all attribtues of a sequence and
# adds it to database '$annotationDirName/annotation.dat'.
# Given attribute hash is stored as hash-dump.
sub _printAnnotation{
    my ($annotationDirName,$h) = @_;
    # create new Berkeley_DB 
    my %database;
    tie %database, 'DB_File', "$annotationDirName/annotation.dat" or d
+ie "Can't initialize database: $!\n";
    my $dump = Data::Dumper->new([$h],[qw($annotation)])->Purity(1)->D
+ump();
    $database{$h->{'id'}} = $dump;
    untie %database;
}

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In reply to DB_File/BerkeleyDB with large datafiles by Lowry76

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