Useless use of numeric gt (>) in void context and Useless use of private variable in void context (Modified by vincenza maselli)

[vincenza maselli]

Hi all,
 I don't have underlined the row 382 because it seems irrilevant (for 
me) and so I have forget it! Sorry. Thank you,
Vincenza

		# 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,
					bla bla bla
																	);
				$dbh->get_GeneRegionAdaptor->store($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);
					}
#this is the line
382				}

			} #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
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