use Bio::Phenotype::OMIM::OMIMparser;

$omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap  => "genemap",
                                                        -omimtext => "omim.txt" );

my $parsedOMIM="parsed.OMIM.txt";
open my $fh, ">", $parsedOMIM or die "Can't open $parsedOMIM: $!";
print $fh "ID" . "\t" . "Disease" . "\t" . "Genes" . "\n";

while ( my $omim_entry = $omim_parser->next_phenotype() ) {
    # This prints everything.
    #~ print( $omim_entry->to_string() );
    #~ print "\n\n";

    # This gets individual data (some of them object-arrays)
    # (and illustrates the relevant methods of OMIMentry).
    my $numb  = $omim_entry->MIM_number();                     # *FIELD* NO
    my $title = $omim_entry->title();                          # *FIELD* TI - first line
    my $alt   = $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - additional lines
    my $mtt   = $omim_entry->more_than_two_genes();            # "#" before title
    my $sep   = $omim_entry->is_separate();                    # "*" before title
    my $desc  = $omim_entry->description();                    # *FIELD* TX
    my $mm    = $omim_entry->mapping_method();                 # from genemap
    my $gs    = $omim_entry->gene_status();                    # from genemap
    my $cr    = $omim_entry->created();                        # *FIELD* CD
    my $cont  = $omim_entry->contributors();                   # *FIELD* CN
    my $ed    = $omim_entry->edited();                         # *FIELD* ED
    my $sa    = $omim_entry->additional_references();          # *FIELD* SA
    my $cs    = $omim_entry->clinical_symptoms_raw();          # *FIELD* CS
    my $comm  = $omim_entry->comment();                        # from genemap

    my $mini_mim   = $omim_entry->miniMIM();                   # *FIELD* MN
      # A Bio::Phenotype::OMIM::MiniMIMentry object.
      # class Bio::Phenotype::OMIM::MiniMIMentry
      # provides the following:
      # - description()
      # - created()
      # - contributors()
      # - edited()
      #
    # Prints the contents of the MINI MIM entry (most OMIM entries do
    # not have MINI MIM entries, though).
    #~ print $mini_mim->description()."\n";
    #~ print $mini_mim->created()."\n";
    #~ print $mini_mim->contributors()."\n";
    #~ print $mini_mim->edited()."\n";

    my @corrs      = $omim_entry->each_Correlate();            # from genemap
      # Array of Bio::Phenotype::Correlate objects.
      # class Bio::Phenotype::Correlate
      # provides the following:
      # - name()
      # - description() (not used)
      # - species() (always mouse)
      # - type() ("OMIM mouse correlate")
      # - comment()

    my @refs       = $omim_entry->each_Reference();            # *FIELD* RF
      # Array of Bio::Annotation::Reference objects.


    my @avs        = $omim_entry->each_AllelicVariant();       # *FIELD* AV
      # Array of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects.
      # class Bio::Phenotype::OMIM::OMIMentryAllelicVariant
      # provides the following:
      # - number (e.g ".0001" )
      # - title (e.g "ALCOHOL INTOLERANCE" )
      # - symbol (e.g "ALDH2*2" )
      # - description (e.g "The ALDH2*2-encoded protein has a change ..." )
      # - aa_ori  (used if information in the form "LYS123ARG" is found)
      # - aa_mut (used if information in the form "LYS123ARG" is found)
      # - position (used if information in the form "LYS123ARG" is found)
      # - additional_mutations (used for e.g. "1-BP DEL, 911T")

    my @cps        = $omim_entry->each_CytoPosition();         # from genemap
      # Array of Bio::Map::CytoPosition objects.

    my @gss        = $omim_entry->each_gene_symbol();          # from genemap
      # Array of strings.

    ### A handy string to store gene symbols
    my $geneSymbols = join(",", @gss);

    ### My query (this is just an example, I actually need to perform more complex queries)

    if ($title =~ /^#/) {
        print $fh $numb . "\t" . $title . "\t" . $geneSymbols . "\n";
    }
}
close $fh;