From fceaf096d75a0a2348365ee76625293ebe20dece Mon Sep 17 00:00:00 2001
From: Dan Staines <dstaines@ebi.ac.uk>
Date: Mon, 5 Nov 2012 09:58:27 +0000
Subject: [PATCH] reformatted to use new perltidy options

---
 modules/t/gene.t | 546 ++++++++++++++++++++++-------------------------
 1 file changed, 251 insertions(+), 295 deletions(-)

diff --git a/modules/t/gene.t b/modules/t/gene.t
index 121ccd40a1..37b4c7848b 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -16,97 +16,92 @@ use Bio::EnsEMBL::DnaDnaAlignFeature;
 # switch on the debug prints
 our $verbose = 0;
 
-debug( "Startup test" );
+debug("Startup test");
 ok(1);
 
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
 
-my $db = $multi->get_DBAdaptor( "core" );
+my $db = $multi->get_DBAdaptor("core");
 
-debug( "Test database instatiated" );
-ok( $db );
+debug("Test database instatiated");
+ok($db);
 
 my $gene;
 my $ga = $db->get_GeneAdaptor();
 
-debug ("Gene->list_dbIDs");
+debug("Gene->list_dbIDs");
 my $ids = $ga->list_dbIDs();
-ok (@{$ids});
+ok(@{$ids});
 
-debug ("Gene->list_stable_ids");
+debug("Gene->list_stable_ids");
 my $stable_ids = $ga->list_stable_ids();
-ok (@{$stable_ids});
+ok(@{$stable_ids});
 
+$gene = $ga->fetch_by_display_label("T9S4_HUMAN");
+ok($gene && $gene->dbID() == 18262);
 
-$gene = $ga->fetch_by_display_label( "T9S4_HUMAN" );
-ok( $gene && $gene->dbID() == 18262 );
-
-$gene = $ga->fetch_by_stable_id( "ENSG00000171456" );
-debug( "Gene->fetch_by_stable_id()" );
-ok( $gene );
-
-my @date_time = localtime( $gene->created_date());
-ok( $date_time[3] == 6 && $date_time[4] == 11 && $date_time[5] == 104 );
+$gene = $ga->fetch_by_stable_id("ENSG00000171456");
+debug("Gene->fetch_by_stable_id()");
+ok($gene);
 
-@date_time = localtime( $gene->modified_date());
-ok( $date_time[3] == 6 && $date_time[4] == 11 && $date_time[5] == 104 );
+my @date_time = localtime($gene->created_date());
+ok($date_time[3] == 6 && $date_time[4] == 11 && $date_time[5] == 104);
 
-debug( "Gene dbID: ". $gene->dbID());
-ok( $gene->dbID() == 18267 );
+@date_time = localtime($gene->modified_date());
+ok($date_time[3] == 6 && $date_time[4] == 11 && $date_time[5] == 104);
 
-debug( "Gene start: ".$gene->start );
-ok( $gene->start() == 30735607 );
+debug("Gene dbID: " . $gene->dbID());
+ok($gene->dbID() == 18267);
 
-debug( "Gene end: ".$gene->end );
-ok( $gene->end() == 30815178 );
+debug("Gene start: " . $gene->start);
+ok($gene->start() == 30735607);
 
-debug( "Gene external name: " . $gene->external_name );
-ok( $gene->external_name eq "Q9H466");
+debug("Gene end: " . $gene->end);
+ok($gene->end() == 30815178);
 
-debug( "Gene external dbname: " . $gene->external_db );
-ok( $gene->external_db eq "Uniprot/SPTREMBL");
+debug("Gene external name: " . $gene->external_name);
+ok($gene->external_name eq "Q9H466");
 
-debug( "Gene display xref id: " . $gene->display_xref->dbID );
-ok( $gene->display_xref->dbID() == 128324);
+debug("Gene external dbname: " . $gene->external_db);
+ok($gene->external_db eq "Uniprot/SPTREMBL");
 
+debug("Gene display xref id: " . $gene->display_xref->dbID);
+ok($gene->display_xref->dbID() == 128324);
 
 # test the getters and setters
-ok( test_getter_setter( $gene, "external_name", "banana" ));   
-ok( test_getter_setter( $gene, "external_db", "dummy" ));   
-ok( test_getter_setter( $gene, "display_xref", 42 ));   
-ok( test_getter_setter( $gene, "created_date", time() ));
-ok( test_getter_setter( $gene, "modified_date", time() ));
+ok(test_getter_setter($gene, "external_name", "banana"));
+ok(test_getter_setter($gene, "external_db",   "dummy"));
+ok(test_getter_setter($gene, "display_xref",  42));
+ok(test_getter_setter($gene, "created_date",  time()));
+ok(test_getter_setter($gene, "modified_date", time()));
 
 my $links = $gene->get_all_DBLinks();
-debug( "Links: ".scalar( @$links ));
+debug("Links: " . scalar(@$links));
 
-ok( scalar @$links == 6 );
+ok(scalar @$links == 6);
 
 SKIP: {
   my $compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor('multi', 'compara', 1);
-  skip 'No comapra database adaptor found', 1 if ! $compara_dba;
+  skip 'No comapra database adaptor found', 1 if !$compara_dba;
   my $homologies = $gene->get_all_homologous_Genes();
-  debug( "Homologies: ".scalar( @$homologies ));
+  debug("Homologies: " . scalar(@$homologies));
 
-  ok( scalar @$homologies ? 
-             ($homologies->[0][0]->isa("Bio::EnsEMBL::Gene")) : 1 );
-};
+  ok(scalar @$homologies ? ($homologies->[0][0]->isa("Bio::EnsEMBL::Gene")) : 1);
+}
 # now create a new gene ...
 
-
 my $sa = $db->get_SliceAdaptor();
 
-my $slice = $sa->fetch_by_region( "chromosome", "20", 30_249_935, 31_254_640 );
+my $slice = $sa->fetch_by_region("chromosome", "20", 30_249_935, 31_254_640);
 
-debug( "Slice from SliceAdaptor" );
+debug("Slice from SliceAdaptor");
 ok($slice);
 
-my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name("ensembl");
+my $analysis   = $db->get_AnalysisAdaptor->fetch_by_logic_name("ensembl");
 my $f_analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name("Vertrna");
-debug( "Analysis from AnalysisAdaptor" );
+debug("Analysis from AnalysisAdaptor");
 ok($analysis);
 
-
 $gene = Bio::EnsEMBL::Gene->new();
 
 my $transcript1 = Bio::EnsEMBL::Transcript->new();
@@ -114,21 +109,20 @@ $transcript1->analysis($analysis);
 my $transcript2 = Bio::EnsEMBL::Transcript->new();
 $transcript2->analysis($analysis);
 
-my $ex1 = Bio::EnsEMBL::Exon->new(); 
+my $ex1 = Bio::EnsEMBL::Exon->new();
 my $ex2 = Bio::EnsEMBL::Exon->new();
 my $ex3 = Bio::EnsEMBL::Exon->new();
 
 my $translation1 = Bio::EnsEMBL::Translation->new();
-my $translation2 = Bio::EnsEMBL::Translation->new();	
+my $translation2 = Bio::EnsEMBL::Translation->new();
 
 ok($gene);
 
-
-$ex1->start( 13586 );
-$ex1->end( 13735 );
+$ex1->start(13586);
+$ex1->end(13735);
 $ex1->phase(0);
-$ex1->end_phase( 0 );
-$ex1->slice( $slice );
+$ex1->end_phase(0);
+$ex1->slice($slice);
 $ex1->strand(1);
 $ex1->analysis($analysis);
 
@@ -136,94 +130,89 @@ my @feats;
 my $fp = new Bio::EnsEMBL::FeaturePair;
 
 $fp->start(13586);
-$fp->end  (13705);
+$fp->end(13705);
 $fp->strand(1);
 $fp->score(10);
 $fp->slice($slice);
 $fp->hstart(100);
-$fp->hend    (219);
-$fp->hstrand (1);
+$fp->hend(219);
+$fp->hstrand(1);
 $fp->hseqname('dummy-hid');
 
-push(@feats,$fp);
-
+push(@feats, $fp);
 
 $fp = new Bio::EnsEMBL::FeaturePair;
 $fp->start(13707);
-$fp->end  (13735);
+$fp->end(13735);
 $fp->strand(1);
 $fp->score(10);
 $fp->slice($slice);
 
-$fp->hstart  (220);
-$fp->hend    (248);
-$fp->hstrand (1);
+$fp->hstart(220);
+$fp->hend(248);
+$fp->hstrand(1);
 $fp->hseqname('dummy-hid');
-push(@feats,$fp);
+push(@feats, $fp);
 
 #
 #
 # 2 Test DnaDnaAlignFeature::new(-features)
 #
-my $dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new( -features => \@feats );
-$dnaf->analysis( $f_analysis );
-
-$ex1->add_supporting_features( $dnaf );
-
+my $dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new(-features => \@feats);
+$dnaf->analysis($f_analysis);
 
+$ex1->add_supporting_features($dnaf);
 
 $ex2->start(201372);
 $ex2->end(201571);
 $ex2->phase(0);
-$ex2->end_phase( -1 );
-$ex2->slice( $slice );
+$ex2->end_phase(-1);
+$ex2->slice($slice);
 $ex2->strand(1);
 $ex2->analysis($analysis);
 
 @feats = ();
-$fp = new Bio::EnsEMBL::FeaturePair;
+$fp    = new Bio::EnsEMBL::FeaturePair;
 
 $fp->start(201372);
-$fp->end  (201471);
+$fp->end(201471);
 $fp->strand(1);
 $fp->score(10);
-$fp->slice( $slice );
+$fp->slice($slice);
 $fp->hstart(100);
-$fp->hend    (199);
-$fp->hstrand (1);
+$fp->hend(199);
+$fp->hstrand(1);
 $fp->hseqname('dummy-hid');
 
-push(@feats,$fp);
-
+push(@feats, $fp);
 
 $fp = new Bio::EnsEMBL::FeaturePair;
 $fp->start(201472);
-$fp->end  (201571);
+$fp->end(201571);
 $fp->strand(1);
 $fp->score(10);
-$fp->slice( $slice );
-
+$fp->slice($slice);
 
-$fp->hstart  (201);
-$fp->hend    (300);
-$fp->hstrand (1);
+$fp->hstart(201);
+$fp->hend(300);
+$fp->hstrand(1);
 $fp->hseqname('dummy-hid');
-push(@feats,$fp);
+push(@feats, $fp);
 
 #
 #
 # 2 Test DnaDnaAlignFeature::new(-features)
 #
-$dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new( -features => \@feats );
-$dnaf->analysis( $f_analysis );
+$dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new(-features => \@feats);
+$dnaf->analysis($f_analysis);
 
-$ex2->add_supporting_features( $dnaf );
+$ex2->add_supporting_features($dnaf);
 
 $ex3->start(210600);
 $ex3->end(210800);
 $ex3->phase(-1);
-$ex3->end_phase( -1 );
-$ex3->slice( $slice );
+$ex3->end_phase(-1);
+$ex3->slice($slice);
 $ex3->strand(1);
 $ex3->analysis($analysis);
 
@@ -235,7 +224,6 @@ $translation1->start(1);
 $translation1->end(150);
 $transcript1->translation($translation1);
 
-
 $transcript2->add_Exon($ex1);
 $transcript2->add_Exon($ex2);
 $transcript2->add_Exon($ex3);
@@ -245,57 +233,56 @@ $translation2->start(1);
 $translation2->end(180);
 $transcript2->translation($translation2);
 
-debug( "Transcripts created" );
+debug("Transcripts created");
 ok($transcript1);
 
-
 $gene->add_Transcript($transcript1);
 $gene->add_Transcript($transcript2);
 
 $gene->analysis($analysis);
 
-debug( "Getting all the Transcripts/Exons from new Gene" );
+debug("Getting all the Transcripts/Exons from new Gene");
 
-my $count = 0;
-my $translates  = 1;
+my $count      = 0;
+my $translates = 1;
 
-foreach my $tr( @{$gene->get_all_Transcripts()} ) {
-  if( $tr->translate()->seq() =~ /\*./ ) {
-    $translates = 0;
-    debug( "Translate failed." );
+foreach my $tr (@{$gene->get_all_Transcripts()}) {
+  if ($tr->translate()->seq() =~ /\*./) {
+	$translates = 0;
+	debug("Translate failed.");
+  }
+  debug("Translation: " . $tr->translate()->seq());
+  foreach my $exon (@{$tr->get_all_Exons()}) {
+	debug("  Exon start: " . $exon->start());
+	debug("  Exon end:   " . $exon->end());
+	debug("  Exon strand " . $exon->strand());
+	$count++;
   }
-  debug( "Translation: ".$tr->translate()->seq() );
-  foreach my $exon ( @{$tr->get_all_Exons()} ) {
-    debug( "  Exon start: ". $exon->start());
-    debug( "  Exon end:   ". $exon->end() );
-    debug( "  Exon strand ".$exon->strand() );
-    $count++;
-  }	
 }
 
 ok($count == 5);
-ok( $translates );
+ok($translates);
 
-ok( scalar(@{$gene->get_all_Exons()} ) == 3);
+ok(scalar(@{$gene->get_all_Exons()}) == 3);
 
-$gene = $gene->transform( "chromosome" );
+$gene = $gene->transform("chromosome");
 
-my $desc = 'test description for a gene';
+my $desc      = 'test description for a gene';
 my $stable_id = 'ENSG00000171456';
 $gene->description($desc);
 $gene->stable_id($stable_id);
 
-$multi->hide( "core", "meta_coord", "gene", "transcript", "exon", "exon_transcript", "translation", "supporting_feature", "dna_align_feature" );
+$multi->hide("core", "meta_coord", "gene", "transcript", "exon", "exon_transcript", "translation", "supporting_feature", "dna_align_feature");
 
 my $gene_ad = $db->get_GeneAdaptor();
-debug( "Storing the gene" );
+debug("Storing the gene");
 $gene_ad->store($gene);
 
 ok(1);
 
 my $genes = $slice->get_all_Genes();
 
-ok(scalar( @$genes) == 1 );
+ok(scalar(@$genes) == 1);
 
 my $gene_out = $genes->[0];
 
@@ -307,35 +294,31 @@ ok($gene_out->description eq $desc);
 
 ok(scalar(@{$gene_out->get_all_Exons()}) == 3);
 
-
-foreach my $tr( @{$gene_out->get_all_Transcripts()} ) {
-  debug( "NewTranscript: ".$tr->dbID() );
-  foreach my $exon ( @{$tr->get_all_Exons()} ) {
-    debug( "  NewExon: ".$exon->start(). " ".$exon->end()." ".$exon->strand());
-  }	
+foreach my $tr (@{$gene_out->get_all_Transcripts()}) {
+  debug("NewTranscript: " . $tr->dbID());
+  foreach my $exon (@{$tr->get_all_Exons()}) {
+	debug("  NewExon: " . $exon->start() . " " . $exon->end() . " " . $exon->strand());
+  }
 }
 
 my $exons = $gene_out->get_all_Transcripts()->[0]->get_all_Exons();
 
-ok( $exons->[0]->start == 13586 );
-
-
-ok( $exons->[1]->strand == 1 );
-ok( $exons->[1]->phase == 0 );
-
+ok($exons->[0]->start == 13586);
 
+ok($exons->[1]->strand == 1);
+ok($exons->[1]->phase == 0);
 
 my $pep;
 my $translate = 0;
-foreach my $trans( @{$gene_out->get_all_Transcripts()} ){
+foreach my $trans (@{$gene_out->get_all_Transcripts()}) {
 
   my $pep = $trans->translate();
-  debug( "Peptide: ".$pep->seq() );
+  debug("Peptide: " . $pep->seq());
 
-  if($pep->seq !~ /\*./){
-    $translate = 1;
+  if ($pep->seq !~ /\*./) {
+	$translate = 1;
   } else {
-    $translate = 0;
+	$translate = 0;
   }
 }
 
@@ -343,85 +326,80 @@ ok($translate == 1);
 
 my $t = $gene_out->get_all_Transcripts()->[1];
 
-my $e = $t->get_all_Exons()->[0];
+my $e  = $t->get_all_Exons()->[0];
 my $se = $e->get_all_supporting_features();
 
-debug( "Got ".scalar( @$se )." supporting features." );
-ok( scalar( @$se ) == 1 );
-
-my $se_start = $se->[0]->start(); 
+debug("Got " . scalar(@$se) . " supporting features.");
+ok(scalar(@$se) == 1);
 
+my $se_start = $se->[0]->start();
 
 my $se_end = $se->[0]->end();
 
+debug("Supporting start $se_start, end $se_end");
+debug("Exon start " . $e->start() . " end " . $e->end());
 
-debug( "Supporting start $se_start, end $se_end" );
-debug( "Exon start ".$e->start()." end ".$e->end() );
-
-ok( $se_start == $e->start() );
-ok( $se_end == $e->end() );
-
+ok($se_start == $e->start());
+ok($se_end == $e->end());
 
 my $pep1 = $t->translate()->seq();
 
 $e->phase(1);
 my $pep2 = $t->translate()->seq();
 
-debug( "Pep phase 0: $pep1" );
-debug( "Pep phase 1: $pep2" );
+debug("Pep phase 0: $pep1");
+debug("Pep phase 1: $pep2");
 
-ok( $pep1 ne $pep2 );
-debug( "checking external references" );
+ok($pep1 ne $pep2);
+debug("checking external references");
 
 $multi->restore();
 
-$slice = $db->get_SliceAdaptor()->fetch_by_region
-  ( "chromosome", "20", 30_252_000, 31_252_001 );
+$slice = $db->get_SliceAdaptor()->fetch_by_region("chromosome", "20", 30_252_000, 31_252_001);
 
-my $known = 0;
+my $known   = 0;
 my $unknown = 0;
 
 $genes = $slice->get_all_Genes();
-for my $gene ( @$genes ) {
-  if( $gene->is_known() ) {
-    $known++;
+for my $gene (@$genes) {
+  if ($gene->is_known()) {
+	$known++;
   } else {
-    $unknown++;
+	$unknown++;
   }
 }
 
-debug( "known: $known Unknown: $unknown\n" );
+debug("known: $known Unknown: $unknown\n");
 
-ok( $known==17 );
+ok($known == 17);
 
 #save contents of gene table
 $multi->save('core', 'gene');
 
 # tests for update method
 # go get a fresh gene again
-$gene = $ga->fetch_by_stable_id( "ENSG00000171456" ); 
+$gene = $ga->fetch_by_stable_id("ENSG00000171456");
 
 # the first update should no effect
 $ga->update($gene);
 
-my $newgene = $ga->fetch_by_stable_id( "ENSG00000171456" ); 
-ok ( $newgene->display_xref->dbID() == 128324 );
-ok ( $newgene->biotype eq 'protein_coding' );
+my $newgene = $ga->fetch_by_stable_id("ENSG00000171456");
+ok($newgene->display_xref->dbID() == 128324);
+ok($newgene->biotype eq 'protein_coding');
 
 # now change the original gene and update it
-my $dbEntryAdaptor=  $db->get_DBEntryAdaptor();
+my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
 
-$gene->display_xref( $dbEntryAdaptor->fetch_by_dbID( 614 ));
+$gene->display_xref($dbEntryAdaptor->fetch_by_dbID(614));
 $gene->biotype('dummy');
 $ga->update($gene);
 
-$newgene = $ga->fetch_by_stable_id( "ENSG00000171456" );
-ok ( $newgene->display_xref->dbID() == 614 );
-ok ( $newgene->biotype eq 'dummy' );
+$newgene = $ga->fetch_by_stable_id("ENSG00000171456");
+ok($newgene->display_xref->dbID() == 614);
+ok($newgene->biotype eq 'dummy');
 
 $multi->restore('core', 'gene');
 
-
 #
 # test GeneAdaptor::fetch_all_by_domain
 #
@@ -431,11 +409,8 @@ debug("Fetch by domain 'IPR000010'");
 
 ok(@genes == 2);
 debug("Got " . scalar(@genes) . " genes");
-ok(($genes[0]->stable_id() eq 'ENSG00000131044') ||
-   ($genes[1]->stable_id() eq 'ENSG00000131044'));
-ok(($genes[0]->stable_id() eq 'ENSG00000174873') ||
-   ($genes[1]->stable_id() eq 'ENSG00000174873'));
-
+ok(($genes[0]->stable_id() eq 'ENSG00000131044') || ($genes[1]->stable_id() eq 'ENSG00000131044'));
+ok(($genes[0]->stable_id() eq 'ENSG00000174873') || ($genes[1]->stable_id() eq 'ENSG00000174873'));
 
 #
 # test GeneAdaptor::fetch_all_by_external_name
@@ -446,31 +421,31 @@ ok(($genes[0]->stable_id() eq 'ENSG00000174873') ||
 debug($gene->stable_id);
 ok($gene->stable_id() eq 'ENSG00000101367');
 
-# 
+#
 # test fetch_all_by_external_name with wildcard restrictions
 #
-(@genes) = @{ $ga->fetch_all_by_external_name('AF_%')};
+(@genes) = @{$ga->fetch_all_by_external_name('AF_%')};
 # Should = 0 because _ is auto-escaped.
-debug('Genes found under external_name AF_%: '.scalar(@genes));
+debug('Genes found under external_name AF_%: ' . scalar(@genes));
 ok(scalar(@genes) == 0);
-(@genes) = @{ $ga->fetch_all_by_external_name('AF_%',undef,'override')};
-debug('Genes found under external_name AF_% with override on: '.scalar(@genes));
+(@genes) = @{$ga->fetch_all_by_external_name('AF_%', undef, 'override')};
+debug('Genes found under external_name AF_% with override on: ' . scalar(@genes));
 debug($genes[0]->stable_id());
 debug($genes[1]->stable_id());
 debug($genes[2]->stable_id());
 debug($genes[3]->stable_id());
 # Note that 9 AF_% xrefs correspond to 4 unique ensembl IDs.
 ok(scalar(@genes) == 4);
-# 
+#
 # test fetch_all_by_external_name with wildcard matching
 #
 @genes = @{$ga->fetch_all_by_external_name('MAE__HUMAN')};
-debug("Wildcard test:".$genes[0]->stable_id);
+debug("Wildcard test:" . $genes[0]->stable_id);
 ok($genes[0]->stable_id() eq 'ENSG00000101367');
 
 @genes = @{$ga->fetch_all_by_external_name('M_%')};
-debug("Wildcard test:". $genes[0]->stable_id() );
-debug(scalar @genes." genes found");
+debug("Wildcard test:" . $genes[0]->stable_id());
+debug(scalar @genes . " genes found");
 ok(scalar @genes == 2);
 
 # Test performance protection (very vague queries return no hits)
@@ -478,10 +453,10 @@ debug("Testing vague query protection");
 {
   my $warnings = q{};
   local $SIG{'__WARN__'} = sub {
-    $warnings .= $_[0];
+	$warnings .= $_[0];
   };
-  ok(scalar (@{$ga->fetch_all_by_external_name('M%')}) == 0);
-  ok(scalar (@{$ga->fetch_all_by_external_name('%')}) == 0);
+  ok(scalar(@{$ga->fetch_all_by_external_name('M%')}) == 0);
+  ok(scalar(@{$ga->fetch_all_by_external_name('%')}) == 0);
   like($warnings, qr/is too vague and will monopolise database/, 'Checking for warnings being emitted by the above methods');
 }
 
@@ -501,34 +476,34 @@ ok($gene->display_id eq $gene->stable_id);
 debug("Test fetch_all_by_biotype");
 @genes = @{$ga->fetch_all_by_biotype('protein_coding')};
 ok(@genes == 20);
-@genes = @{$ga->fetch_all_by_biotype(['protein_coding','sRNA'])};
+@genes = @{$ga->fetch_all_by_biotype(['protein_coding', 'sRNA'])};
 ok(@genes == 20);
 
 #
 # test Gene: get_all_alt_alleles
 #
 
-$gene = $ga->fetch_by_dbID( 18256 );
+$gene = $ga->fetch_by_dbID(18256);
 my $alt_genes = $gene->get_all_alt_alleles();
 
-ok( $gene->is_reference == 1);
+ok($gene->is_reference == 1);
 
-ok( scalar( @$alt_genes ) == 3 );
+ok(scalar(@$alt_genes) == 3);
 
 # expect the following alleles
-my %gene_ids = ( 18257 => 1, 18258 => 1, 18259 => 1);
+my %gene_ids = (18257 => 1, 18258 => 1, 18259 => 1);
 my $ok = 1;
-for my $gene ( @$alt_genes ) {
+for my $gene (@$alt_genes) {
   $ok = $ok && $gene_ids{$gene->dbID()};
   $ok = $ok && !($gene->is_reference);
 }
-ok( $ok );
+ok($ok);
 
 #
 # test storing a new allele group
 #
 
-$multi->hide( 'core', 'alt_allele' );
+$multi->hide('core', 'alt_allele');
 
 #TODO Fix. Code current raises this warning. Don't use alt genes on a ref slice or change the code
 #
@@ -540,58 +515,55 @@ $multi->hide( 'core', 'alt_allele' );
 #---------------------------------------------------
 
 my @alt_genes;
-push( @alt_genes, $ga->fetch_by_dbID(18270) );
-push( @alt_genes, $ga->fetch_by_dbID(18271) );
-push( @alt_genes, $ga->fetch_by_dbID(18272) );
-
-capture_std_streams(sub {
-  my ($stdout_ref, $stderr_ref) = @_;
-  $ga->store_alt_alleles( \@alt_genes );
-  my $check = qr/.+ alternative .+ reference sequence .+ Ignoring/;
-  like(${$stderr_ref}, $check, 'Checking we are still warning about multiple alt_alleles on refs');
-});
-$gene = $ga->fetch_by_dbID( 18270 );
+push(@alt_genes, $ga->fetch_by_dbID(18270));
+push(@alt_genes, $ga->fetch_by_dbID(18271));
+push(@alt_genes, $ga->fetch_by_dbID(18272));
+
+capture_std_streams(
+  sub {
+	my ($stdout_ref, $stderr_ref) = @_;
+	$ga->store_alt_alleles(\@alt_genes);
+	my $check = qr/.+ alternative .+ reference sequence .+ Ignoring/;
+	like(${$stderr_ref}, $check, 'Checking we are still warning about multiple alt_alleles on refs');
+  });
+$gene      = $ga->fetch_by_dbID(18270);
 $alt_genes = $gene->get_all_alt_alleles();
-%gene_ids = ( 18271=>1, 18272=>1 );
+%gene_ids  = (18271 => 1, 18272 => 1);
 
 $ok = 1;
-for my $gene ( @$alt_genes ) {
+for my $gene (@$alt_genes) {
   $ok = $ok && $gene_ids{$gene->dbID()};
 }
-ok( $ok );
+ok($ok);
 
 #
 # Gene remove test
 #
 
-$multi->save( "core", "gene", "transcript", 
-	      "translation", "protein_feature",
-	      "exon", "exon_transcript", "supporting_feature",
-	      "object_xref", "ontology_xref", "identity_xref",
-        "dna_align_feature", "protein_align_feature");
+$multi->save("core", "gene", "transcript", "translation", "protein_feature", "exon", "exon_transcript", "supporting_feature", "object_xref", "ontology_xref", "identity_xref", "dna_align_feature", "protein_align_feature");
 
-$gene = $ga->fetch_by_stable_id( "ENSG00000171456" );
+$gene = $ga->fetch_by_stable_id("ENSG00000171456");
 
-my $gene_count = count_rows( $db, "gene" );
-my $exon_count = count_rows( $db, "exon" );
-my $trans_count = count_rows( $db, "transcript" );
-my $tl_count = count_rows( $db, "translation" );
+my $gene_count  = count_rows($db, "gene");
+my $exon_count  = count_rows($db, "exon");
+my $trans_count = count_rows($db, "transcript");
+my $tl_count    = count_rows($db, "translation");
 
-my $tminus = scalar( @{$gene->get_all_Transcripts() } );
-my $eminus = scalar( @{$gene->get_all_Exons() } );
+my $tminus = scalar(@{$gene->get_all_Transcripts()});
+my $eminus = scalar(@{$gene->get_all_Exons()});
 
-debug( "Genes before ".$gene_count );
-debug( "Exons before ".$exon_count );
-debug( "Transcripts before ".$trans_count );
-debug( "Translations before ".$tl_count );
-debug( "Gene has ".$tminus." transcripts" );
-debug( "Gene has ".$eminus." exons" );
+debug("Genes before " . $gene_count);
+debug("Exons before " . $exon_count);
+debug("Transcripts before " . $trans_count);
+debug("Translations before " . $tl_count);
+debug("Gene has " . $tminus . " transcripts");
+debug("Gene has " . $eminus . " exons");
 
-$ga->remove( $gene );
+$ga->remove($gene);
 
-ok( count_rows( $db, "gene" ) == ( $gene_count - 1 ));
-ok( count_rows( $db, "transcript" ) == ($trans_count-$tminus));
-ok( count_rows( $db, "exon" ) == ( $exon_count - $eminus ));
+ok(count_rows($db, "gene") ==       ($gene_count - 1));
+ok(count_rows($db, "transcript") == ($trans_count - $tminus));
+ok(count_rows($db, "exon") ==       ($exon_count - $eminus));
 
 ok(!defined($gene->dbID()));
 ok(!defined($gene->adaptor()));
@@ -607,28 +579,24 @@ $gene = Bio::EnsEMBL::Gene->new();
 
 $gene->slice($slice);
 
-my $first_ex = Bio::EnsEMBL::Exon->new
-  (-START => 10,
-   -END   => 100,
-   -STRAND => 1,
-   -PHASE  => 0,
-   -END_PHASE => 1,
-   -SLICE => $slice);
-
-my $second_ex = Bio::EnsEMBL::Exon->new
-  (-START   => 200,
-   -END     => 400,
-   -STRAND  => 1,
-   -PHASE   => 1,
-   -END_PHASE => 0,
-   -SLICE   => $slice);
-
-$transcript1 = Bio::EnsEMBL::Transcript->new
-  (-EXONS => [$first_ex, $second_ex]);
+my $first_ex = Bio::EnsEMBL::Exon->new(-START     => 10,
+									   -END       => 100,
+									   -STRAND    => 1,
+									   -PHASE     => 0,
+									   -END_PHASE => 1,
+									   -SLICE     => $slice);
+
+my $second_ex = Bio::EnsEMBL::Exon->new(-START     => 200,
+										-END       => 400,
+										-STRAND    => 1,
+										-PHASE     => 1,
+										-END_PHASE => 0,
+										-SLICE     => $slice);
+
+$transcript1 = Bio::EnsEMBL::Transcript->new(-EXONS => [$first_ex, $second_ex]);
 $transcript1->analysis($analysis);
 
-$transcript2 = Bio::EnsEMBL::Transcript->new
-  (-EXONS => [$first_ex]);
+$transcript2 = Bio::EnsEMBL::Transcript->new(-EXONS => [$first_ex]);
 $transcript2->analysis($analysis);
 
 $gene->add_Transcript($transcript1);
@@ -637,46 +605,40 @@ $gene->add_Transcript($transcript2);
 $gene->recalculate_coordinates();
 
 ok($gene->start() == 10);
-ok($gene->end()  == 400);
-
+ok($gene->end() == 400);
 
 {
   # Test transformming genes over a gapped alignment, when gaps
   # only occur in introns
   # target_slice = sliceAdaptor->fetch_by_region( "alt_chrom", "gap_map_test" );
 
-  my $gene = $ga->fetch_by_dbID( 18274 );
+  my $gene = $ga->fetch_by_dbID(18274);
   debug(":::: Gene: $gene");
-  my $new_gene = $gene->transform( "alt_chrom" );
+  my $new_gene = $gene->transform("alt_chrom");
   debug(":::: New Gene $new_gene");
-  my $trans_orig = $gene->get_all_Transcripts()->[0];
+  my $trans_orig   = $gene->get_all_Transcripts()->[0];
   my $trans_mapped = $new_gene->get_all_Transcripts()->[0];
-  ok( $trans_orig->spliced_seq() eq 
-      $trans_mapped->spliced_seq());
+  ok($trans_orig->spliced_seq() eq $trans_mapped->spliced_seq());
 
   # the assembly is rigged to have no gaps between the first and second exon
-  ok( $trans_mapped->get_all_Exons()->[0]->end()+1==
-      $trans_mapped->get_all_Exons()->[1]->start() );
+  ok($trans_mapped->get_all_Exons()->[0]->end() + 1 == $trans_mapped->get_all_Exons()->[1]->start());
 }
 
-
 #
 # test that the display_xref_id is set for the gene and its transcript
 #
-$multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
-              "exon_transcript", "translation" );
+$multi->hide("core", "gene", "transcript", "exon", 'xref', 'object_xref', "exon_transcript", "translation");
 
 $gene->analysis($analysis);
 my $analysis_adap = $db->get_AnalysisAdaptor();
 $analysis = $analysis_adap->fetch_by_logic_name("ensembl");
 
 my $dbe = Bio::EnsEMBL::DBEntry->new(-primary_id => 'test_id',
-                                     -version    => 1,
-                                     -dbname     => 'EMBL',
-                                     -release    => 1,
-                                     -display_id => 'test_id',
-	                             -analysis   => $analysis);
-
+									 -version    => 1,
+									 -dbname     => 'EMBL',
+									 -release    => 1,
+									 -display_id => 'test_id',
+									 -analysis   => $analysis);
 
 $gene->add_DBEntry($dbe);
 $gene->display_xref($dbe);
@@ -684,59 +646,54 @@ $gene->display_xref($dbe);
 $gene->get_all_Transcripts()->[0]->add_DBEntry($dbe);
 $gene->get_all_Transcripts()->[0]->display_xref($dbe);
 
-
-debug( "Storing gene" );
+debug("Storing gene");
 $gene_ad->store($gene);
 
-
 my $dbe_id = $db->dbc->db_handle->selectall_arrayref("SELECT display_xref_id FROM gene")->[0]->[0];
 
 ok($dbe_id && $dbe_id == $dbe->dbID());
 
-
-
 $multi->restore();
 
-
 #
 # tests for multiple versions of genes in a database
 #
 
 $gene = $ga->fetch_by_stable_id('ENSG00000355555');
 debug("fetch_by_stable_id");
-ok( $gene->dbID == 18275 );
+ok($gene->dbID == 18275);
 
-@genes = @{ $ga->fetch_all_versions_by_stable_id('ENSG00000355555') };
+@genes = @{$ga->fetch_all_versions_by_stable_id('ENSG00000355555')};
 debug("fetch_all_versions_by_stable_id");
-ok( scalar(@genes) == 1 );
+ok(scalar(@genes) == 1);
 
 my $sl = $sa->fetch_by_region('chromosome', 'MT_NC_001807');
-@genes = @{ $sl->get_all_Genes };
-ok( scalar(@genes) == 1 );
+@genes = @{$sl->get_all_Genes};
+ok(scalar(@genes) == 1);
 
 $gene = $ga->fetch_by_transcript_stable_id('ENST00000355555');
 debug("fetch_by_transcript_stable_id");
-ok( $gene->dbID == 18275 );
+ok($gene->dbID == 18275);
 
 $gene = $ga->fetch_by_translation_stable_id('ENSP00000355555');
 debug("fetch_by_translation_stable_id");
-ok( $gene->dbID == 18275 );
+ok($gene->dbID == 18275);
 
 $gene = $ga->fetch_by_exon_stable_id('ENSE00001109603');
 debug("fetch_by_exon_stable_id");
-ok( $gene->dbID == 18275 );
+ok($gene->dbID == 18275);
 
-@genes = @{ $ga->fetch_all_by_external_name('PAL2_HUMAN') };
-debug( "fetch_all_by_external_name" );
-ok( scalar(@genes) == 1 && $genes[0]->dbID == 18264 );
+@genes = @{$ga->fetch_all_by_external_name('PAL2_HUMAN')};
+debug("fetch_all_by_external_name");
+ok(scalar(@genes) == 1 && $genes[0]->dbID == 18264);
 
 $gene = $ga->fetch_by_display_label('PLAGL2');
 debug("fetch_by_display_label");
-ok( $gene->dbID == 18264 );
+ok($gene->dbID == 18264);
 
 $gene = $ga->fetch_by_dbID(18264);
 debug("fetch_by_dbID, current");
-ok( $gene->is_current == 1 );
+ok($gene->is_current == 1);
 
 #$gene = $ga->fetch_by_dbID(18264);
 #debug("fetch_by_dbID, non current");
@@ -745,12 +702,11 @@ ok( $gene->is_current == 1 );
 # store/update
 
 $gene = $ga->fetch_by_stable_id('ENSG00000355555');
-foreach my $t (@{ $gene->get_all_Transcripts }) {
+foreach my $t (@{$gene->get_all_Transcripts}) {
   $t->get_all_Exons;
 }
 
-$multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
-              "exon_transcript", "translation" );
+$multi->hide("core", "gene", "transcript", "exon", 'xref', 'object_xref', "exon_transcript", "translation");
 
 $gene->version(3);
 $gene->dbID(undef);
@@ -766,7 +722,7 @@ $ga->store($gene);
 $gene = $ga->fetch_by_stable_id('ENSG00000355555');
 ok($gene->is_current == 1);
 
-@genes = @{ $ga->fetch_all_versions_by_stable_id('ENSG00000355555') };
+@genes = @{$ga->fetch_all_versions_by_stable_id('ENSG00000355555')};
 foreach my $g (@genes) {
   next unless ($g->version == 4);
   ok($g->is_current == 0);
@@ -797,7 +753,7 @@ $gene->remove_unconventional_transcript_associations();
 ok(@{$gene->get_all_unconventional_transcript_associations()} == 0);
 
 # test adding to a new gene
-my $new_gene = $ga->fetch_by_dbID(18260);
+my $new_gene       = $ga->fetch_by_dbID(18260);
 my $new_transcript = $db->get_TranscriptAdaptor()->fetch_by_dbID(21720);
 
 ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 0);
@@ -822,12 +778,12 @@ ok(@{$utaa->fetch_all_by_gene($new_gene)} == 0);
 
 #testing canonical_transcript information
 $new_gene = $ga->fetch_by_dbID(18256);
-ok($new_gene->canonical_transcript->dbID == 21716);  #test 85
-ok($new_gene->canonical_annotation eq 'longest transcript in gene'); #test 86
+ok($new_gene->canonical_transcript->dbID == 21716);    #test 85
+ok($new_gene->canonical_annotation eq 'longest transcript in gene');    #test 86
 
 #test the get_species_and_object_type method from the Registry
 my $registry = 'Bio::EnsEMBL::Registry';
-my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('ENSG00000355555');
-ok( $species eq 'homo_sapiens' && $object_type eq 'Gene');
+my ($species, $object_type, $db_type) = $registry->get_species_and_object_type('ENSG00000355555');
+ok($species eq 'homo_sapiens' && $object_type eq 'Gene');
 
-done_testing();
\ No newline at end of file
+done_testing();
-- 
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