# parse_genbank
my $file = shift;
my $seqin =  Bio::SeqIO->new(-file   => $file,
                             -format => 'GenBank');
while(my $seq = $seqin->next_seq()){
	foreach my $feat_object ($seq->get_SeqFeatures){
		&decompose_feature($feat_object);
	}
}


# decompose_feature
sub decompose_feature {
	my $feat_object = shift;
 
	# primary_tag = gene
	if($feat_object->primary_tag() eq 'gene'){
		&start_another_gene($feat_object);
		$last_gene_feat = $feat_object;
	# primary_tag = CDS
	}elsif($feat_object->primary_tag() eq 'CDS'){
		# make transcript
		if($last_gene_feat){
			unless(&check_contain_in($last_gene_feat, $feat_object)){
				throw(
				"\nCDS\n".
				"\tstart: ".$feat_object->start. "\n".
				"\tend:   ".$feat_object->end. "\n".
				"is not contained in gene ". $last_gene_feat->start. "-". $last_gene_feat->end. "\n");
		}
	}
	&create_transcript_and_exon($unique_id, 'protein_coding', 'KNOWN', $feat_object);
}


sub create_transcript_and_exon {
	my $unique_id = shift;
	my $type = shift;
	my $status = shift;
	my $feat_object =  shift;
	
	$featurehash{$unique_id}{'type'} = $type;
	$featurehash{$unique_id}{'status'} = $status;

	# make transcript
	my $new_transcript = make_Transcript_object($t_stable_id, $type, $time);
	$featurehash{$unique_id}{'transcript'}{$t_stable_id} = $new_transcript;
	my $desc = get_desc($feat_object);
	$featurehash{$unique_id}{'description'} = $desc;

	# multi exons
	if($feat_object->location->isa('Bio::Location::SplitLocationI')){
		for my $location ( $feat_object->location->sub_Location ) {
			my $exon_start = $location->start;
			my $exon_end = $location->end;
			my $exon_strand = $location->strand;
	
	# make exon
	my $exon = make_Exon_object($featurehash{$unique_id}{'slice'}, $exon_start,
	$exon_end, $exon_strand, $featurehash{$unique_id}{'transcript'}{$t_stable_id},
	$e_stable_id, $time);
	$e_stable_id++;
		}

	# single exon
	}else{
	# make exon
	my $exon = make_Exon_object($featurehash{$unique_id}{'slice'}, $feat_object->start,
	$feat_object->end, $feat_object->strand, $featurehash{$unique_id}{'transcript'}{$t_stable_id},
	$e_stable_id, $time);
	$e_stable_id++;
	}
}


#store annotation
#make gene
my $gene = Bio::EnsEMBL::Gene->new(
        -START     => $feature->{$key}->{'start'},
        -END       => $feature->{$key}->{'end'},
        -STRAND    => $feature->{$key}->{'strand'},
        -SLICE     => $feature->{$key}->{'slice'},
        -ANALYSIS  => create_analysis($LOGIC_NAME_EXON),
        -STABLE_ID => $feature->{$key}->{'stable_id'},
        -VERSION   => $ATTRIBUTE_VERSION,
        -TYPE      => $feature->{$key}->{'type'},
        -DESCRIPTION  => $feature->{$key}->{'description'},
        -STATUS => $feature->{$key}->{'status'},
        -CANONICAL_TRANSCRIPT => $feature->{$key}->{'transcript'}->{$first_transcript},
        -CREATED_DATE => $time,
        -MODIFIED_DATE => $time,
        -SOURCE    => $feature->{$key}->{'source'},
        );

# start to store gene object
my $gene_DB_id = $db->get_GeneAdaptor->store($gene);

# store gene xref
$db->get_DBEntryAdaptor->store($feature->{$key}->{'DBEntry'}, $gene_DB_id, 'Gene');
$gene->display_xref($feature->{$key}->{'DBEntry'});
$db->get_GeneAdaptor->update($gene);

# transcript xref
for my $tran (@{$gene->get_all_Transcripts}) {
	my $DBEntry = Bio::EnsEMBL::DBEntry->new(
		-DBNAME  => $SPE_PREFIX. '_TRANSCRIPT',
		-RELEASE => 1,                                                                        
		-PRIMARY_ID => $feature->{$key}->{'ID'},
		-DISPLAY_ID => $feature->{$key}->{'symbol'},
		-DESCRIPTION=> $META->{'assembly.default'}
		);
	$db->get_DBEntryAdaptor->store($DBEntry, $tran->dbID,'Transcript');
	$tran->display_xref($DBEntry);
	$db->get_TranscriptAdaptor->update($tran);
}