Useless use of numeric gt (>) in void context and Useless use of private variable in void context

[vincenza maselli]

Hi all,
I got this error when run my scripts:
Useless use of numeric gt (>) in void context at 
/Users/vincenza/src/gfdb/modules/Bio/DBLoader.pm line 382.
Useless use of private variable in void context at 
/Users/vincenza/src/gfdb/modules/Bio/DBLoader.pm line 382.
below is the code:

have some of you any suggestion? Thank you,
Vincenza
sub store_gene_region{
        my ($self,$gene_stable_id, $member_obj, $slice) = @_;
        my $dbh = $self->dbh();
        my (@g_regions,$gene_region);
        unless ($slice){
                $slice = $self->_get_slice($member_obj->gene_stable_id);
                
        }
	# store transcript	
	my @transcripts = @{$slice->get_all_Transcripts()};
	unless(@transcripts){print LOG "No transcript 
for\nNA$gene_stable_id\n";return}
	my $gene_region_obj;
	foreach my $transcript(@transcripts){
		my $ontology_trans ;
		my $transcript_start = $transcript->start;
		my $transcript_end = $transcript->end;
		my $transcript_strand = $transcript->strand;
		unless ($transcript->coding_region_start){
			$ontology_trans = 
$dbh->get_OntologyAdaptor->fetch_by_term('pseudogene');
			#print "TERM pseudogene\n";
			$gene_region_obj = Bio::GeneFamilyDB::GeneRegion->new(-MEMBER 	=> 
$member_obj,
																  -GR_START => $transcript_start,
																  -GR_END 	=> $transcript_end,
																  -STRAND 	=> $transcript_strand,
																  -ONTOLOGY	=> $ontology_trans
																);
			$dbh->get_GeneRegionAdaptor->store($gene_region_obj);
			next;
		
		}
		#print "TERM transcript\n";
		$ontology_trans = 
$dbh->get_OntologyAdaptor->fetch_by_term('transcript');
		$gene_region_obj = Bio::GeneFamilyDB::GeneRegion->new(-MEMBER 	=> 
$member_obj,
																  -GR_START => $transcript_start,
																  -GR_END 	=> $transcript_end,
																  -STRAND 	=> $transcript_strand,
																  -ONTOLOGY	=> $ontology_trans
																);
		$dbh->get_GeneRegionAdaptor->store($gene_region_obj);
		
		# store exon
		my @exons = @{$transcript->get_all_Exons()};
		my ($ontology_exon, $exon_start, $exon_end, $exon_strand);
		unless ($transcript->translation){
			foreach my $exon(@exons){
				$exon_start = $exon->start;
				$exon_end = $exon->end;
				$exon_strand = $exon->strand;
				$ontology_exon = 
$dbh->get_OntologyAdaptor->fetch_by_term('noncoding_exon');
				$gene_region_obj = Bio::GeneFamilyDB::GeneRegion->new(-MEMBER 	=> 
$member_obj,
																	  -GR_START => $exon_start,
																	  -GR_END 	=> $exon_end,
																	  -STRAND 	=> $exon_strand,
																	  -ONTOLOGY	=> $ontology_exon
																	);
				$dbh->get_GeneRegionAdaptor->store($gene_region_obj);	
				}
			next;
			
		}
		foreach my $exon(@exons){
			my ($gr_obj,$term);
			my $exon_start = $exon->start;
			my $exon_end = $exon->end;
			my $exon_strand = $exon->strand;
			my $ontology_exon;
			my $coding_start = $transcript->coding_region_start;
			my $coding_end = $transcript->coding_region_end;
			my ($region_start, $region_end);
			if ($exon_strand == 1){
				if ($exon_start >= $coding_start && $exon_end <= $coding_end){
					$term ='exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start <= $coding_start && $exon_end >= $coding_end){
					$term ='exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start < $coding_start && $exon_end < $coding_end){
					$term = 'five_prime_noncoding_exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
					$region_start = $exon_start;
					$region_end = $coding_start;
					$term = 'five_prime_exon_noncoding_region';
					$gr_obj = $self->_get_region_obj($term, $region_start, 
$region_end, $member_obj,$exon_strand);
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start > $coding_start && $exon_end >$coding_end, 
$member_obj,$exon_strand){
					$term = 'three_prime_noncoding_exon';
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
					$region_start = $coding_end;
					$region_end = $exon_end;
					$term = 'three_prime_exon_noncoding_region';
					#print "TERM $term\n";
					$gr_obj = $self->_get_region_obj($term, $region_start, 
$region_end, $member_obj,$exon_strand);
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start > $coding_end && $exon_end > $coding_end){
					$term = 'three_prime_utr';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start < $coding_start && $exon_end < $coding_start){
					$term = 'five_prime_utr';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				else{
					# store utr generic
					my @utrs = $self->_get_utrs($transcript);
					unless (@utrs){next;}
					foreach my $utr (@utrs){
						my $utr_start = $utr->start;
						my $utr_end = $utr->end;
						my $utr_strand = $utr->strand;
						my $ontology_utr = 
$dbh->get_OntologyAdaptor->fetch_by_term('utr');
						#print "TERM utr\n";
						$gene_region_obj = Bio::GeneFamilyDB::GeneRegion->new(-MEMBER 	=> 
$member_obj,
																	  -GR_START => $utr_start,
																	  -GR_END 	=> $utr_end,
																	  -STRAND 	=> $utr_strand,
																	  -ONTOLOGY	=> $ontology_utr
																	);
						my $gr_dbID = 
$dbh->get_GeneRegionAdaptor->store($gene_region_obj);
						my $gr_obj = $dbh->get_GeneRegionAdaptor->fetch_by_dbID($gr_dbID);
						push (@g_regions, $gr_obj);
					}
				}
			} #if strand 1
			elsif ($exon_strand == -1){
				if ($exon_start >= $coding_start && $exon_end <= $coding_end){
					$term ='exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start <= $coding_start && $exon_end >= $coding_end){
					$term ='exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start < $coding_start && $exon_end < $coding_end){
					$term = 'three_prime_noncoding_exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
					$region_start = $exon_start;
					$region_end = $coding_start;
					$term = 'three_prime_exon_noncoding_region';
					$gr_obj = $self->_get_region_obj($term, $region_start, 
$region_end, $member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
					
				}
				elsif ($exon_start > $coding_start && $exon_end >$coding_end){
					$term = 'five_prime_noncoding_exon';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
					$region_start = $coding_end;
					$region_end = $exon_end;	
					$term = 'five_prime_exon_noncoding_region';
					$gr_obj = $self->_get_region_obj($term, $region_start, 
$region_end, $member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start > $coding_end && $exon_end > $coding_end){
					$term = 'five_prime_utr';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				elsif ($exon_start < $coding_start && $exon_end < $coding_start){
					$term = 'three_prime_utr';
					$gr_obj = $self->_get_region_obj($term, $exon_start, $exon_end, 
$member_obj,$exon_strand);
					#print "TERM $term\n";
					push (@g_regions, $gr_obj);
				}
				else{
				# store utr generic
					my @utrs = $self->_get_utrs($transcript);
					unless (@utrs){next;}
					foreach my $utr (@utrs){
						my $utr_start = $utr->start;
						my $utr_end = $utr->end;
						my $utr_strand = $utr->strand;
						my $ontology_utr = 
$dbh->get_OntologyAdaptor->fetch_by_term('utr');
						#print "TERM utr\n";
						$gene_region_obj = Bio::GeneFamilyDB::GeneRegion->new(-MEMBER 	=> 
$member_obj,
																	  -GR_START => $utr_start,
																	  -GR_END 	=> $utr_end,
																	  -STRAND 	=> $utr_strand,
																	  -ONTOLOGY	=> $ontology_utr
																	);
						my $gr_dbID = 
$dbh->get_GeneRegionAdaptor->store($gene_region_obj);
						my $gr_obj = $dbh->get_GeneRegionAdaptor->fetch_by_dbID($gr_dbID);
						push (@g_regions, $gr_obj);
					}
				}
			} # elsif strand -1
		}# foreach exons
						
	}#foreach transcript
		
	return ([EMAIL PROTECTED]);
}

----------------------------------------------------------------------
Ph. D. student
SEMM (European School of Molecular Medicine)
Bioinformatics Code Project
Tigem (Telethon Institute of Genetics and Medicine)
Via Pietro Castellino 111
80131 Napoli, ITALY
Phone 39-081-613-23-39 (direct)
            39-329-321-05-55 (mobile)
Fax       39-081-560-98-77