updated to use patch test database

now fully testing patches and haplotypes

modules/t/assemblyException.t

@@ -12,31 +12,27 @@ our $verbose = 0;
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
 ok(1);
 
-my $db = $multi->get_DBAdaptor('core');
+my $db = $multi->get_DBAdaptor('patch');
 my $sfa = $db->get_SimpleFeatureAdaptor();
 my $aexc_adaptor = $db->get_AssemblyExceptionFeatureAdaptor();
 my $slice_adaptor = $db->get_SliceAdaptor();
 
-##chromosome Y is a fake 'PAR' linked to chromosome 20
-my $slice = $slice_adaptor->fetch_by_region('chromosome', 'Y',8e6,13e6);
+my $slice = $slice_adaptor->fetch_by_region('chromosome', 'Y', 1, 400000);
 my $feats = $sfa->fetch_all_by_Slice($slice);
-debug("Got " . scalar(@$feats));
-ok( @$feats ==58 );
+is( @$feats, 94, "Returned 58 features" );
 
 print_features($feats);
 
 
-#HAP_1 is a fake haplotype on chromosome 20
-$slice = $slice_adaptor->fetch_by_region('chromosome', '20_HAP1',
-                                            30_399_998,30_600_002);
-my $org_slice = $slice_adaptor->fetch_by_region('chromosome', '20',
-                                            30_430_000,30_500_000 );
+$slice = $slice_adaptor->fetch_by_region('chromosome', 'Y',
+                                            1, 200000);
+my $org_slice = $slice_adaptor->fetch_by_region('chromosome', 'X',
+                                            1, 200000);
 
 
 $feats = $sfa->fetch_all_by_Slice($slice);
 
-debug("Got " . scalar(@$feats));
-is( @$feats, 9 , "Fetched 9 features");
+is( @$feats, 24 , "Fetched 24 features");
 
 print_features($feats);
 
@@ -56,13 +52,13 @@ for my $f ( @$feats ) {
 }
 
 
-$slice = $slice_adaptor->fetch_by_region('chromosome', '20_HAP1',
-					 30_400_000,30_600_000);
+$slice = $slice_adaptor->fetch_by_region('chromosome', 'Y',
+					 1, 200000);
 $feats = $sfa->fetch_all_by_Slice( $slice );
 
 debug( "After storing retrieval" );
 print_features($feats);
-is(@$feats, 14, "Fetched 14 features");
+is(@$feats, 24, "Fetched 24 features");
 
 
 
@@ -70,28 +66,27 @@ is(@$feats, 14, "Fetched 14 features");
 # sequence getting tests
 #
 
-my $hap_slice = $slice_adaptor->fetch_by_region('chromosome', '20_HAP1',
-                                             30_400_000,30_700_000 );
+my $hap_slice = $slice_adaptor->fetch_by_region('chromosome', 'Y',
+                                             10001, 400000);
 
-$org_slice = $slice_adaptor->fetch_by_region('chromosome', '20',
-                                             30_400_000,30_800_000 );
+$org_slice = $slice_adaptor->fetch_by_region('chromosome', 'X',
+                                             60001, 400000);
 
 my ( $fhs, $bhs, $fos, $bos );
 
 debug( "Front hap seq: ".($fhs = $hap_slice->subseq( 99_991, 100_000 )));
-debug( "Back hap seq: ".($bhs = $hap_slice->subseq( 200_001, 200_010 )));
+debug( "Back hap seq: ".($bhs = $hap_slice->subseq( 400_001, 400_010 )));
 debug( "Front org seq: ".( $fos = $org_slice->subseq( 99_991, 100_000 )));
-debug( "Back org seq: ".( $bos = $org_slice->subseq( 300_001, 300_010 )));
+debug( "Back org seq: ".( $bos = $org_slice->subseq( 400_001, 400_010 )));
 
-ok( $fhs eq $fos );
-ok( $bhs eq $bos );
+is( $fhs, $fos, "Front sequences for haplotype and reference are the same" );
+is( $bhs, $bos, "Back sequences for haplotype and reference are the same" );
 
 
-$slice = $slice_adaptor->fetch_by_region('chromosome', '20_HAP1',
-					 30_499_998,30_500_002);
+$slice = $slice_adaptor->fetch_by_region('chromosome', 'Y',
+					 299_998, 300_002);
 
-debug($slice->seq);
-is( $slice->seq(), "GTNNN", "Fetched haplotype subslice");
+is( $slice->seq(), "ACAGA", "Fetched haplotype subslice");
 
 $multi->restore();
 

modules/t/assemblyExceptionFeature.t

@@ -13,7 +13,7 @@ my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
 
 # get a core DBAdaptor
 #
-my $dba = $multi->get_DBAdaptor("core");
+my $dba = $multi->get_DBAdaptor("patch");
 my $aefa = $dba->get_AssemblyExceptionFeatureAdaptor();
 ok($aefa);
 
@@ -42,10 +42,19 @@ is(ref($aef->adaptor), 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', "
 
 # fetch all
 my $chr_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome', 
-                                                        '20_HAP1');
+                                                        'Y');
+my $ref_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome', '6');
+my $patch_slice = $dba->get_SliceAdaptor->fetch_by_region('supercontig', 'HG1304_PATCH');
+
 my @features = @{$aefa->fetch_all_by_Slice($chr_slice)};
 
-is(@features, 1, "Fetched one assembly exception feature for 20_HAP1");
+is(@features, 2, "Fetched one assembly exception feature for Y");
+
+my @ref_features = @{$aefa->fetch_all_by_Slice($ref_slice)};
+is(@ref_features, 1, "Fetched one assembly exception features for chromosome 6");
+
+my @patch_features = @{ $aefa->fetch_all_by_Slice($patch_slice) };
+is(@patch_features, 1, "Fetched one assembly exception for HG1304_PATCH");
 
 foreach my $f (@features) {
   debug( "Feature: " . $f->slice->seq_region_name . " " . 
@@ -55,6 +64,22 @@ foreach my $f (@features) {
         $as->start . " " . $as->end);
 }
 
+foreach my $f (@ref_features) {
+  debug( "Feature: " . $f->slice->seq_region_name . " " .
+         $f->start . " " . $f->end . " " . $f->type);
+  my $as = $f->alternate_slice();
+  debug(" Alternate slice: " . $as->seq_region_name . " " .
+        $as->start . " " . $as->end);
+}
+
+foreach my $f (@patch_features) {
+  debug( "Feature: " . $f->slice->seq_region_name . " " .
+         $f->start . " " . $f->end . " " . $f->type);
+  my $as = $f->alternate_slice();
+  debug(" Alternate slice: " . $as->seq_region_name . " " .
+        $as->start . " " . $as->end);
+}
+
 my ($f) = @features;
 is($f->display_id, $f->alternate_slice->seq_region_name, "Feature display id matches feature's alternate slice name");
 
@@ -67,7 +92,7 @@ is($feat->dbID(), 1, "Feature dbID is 1");
 my $aef_store = new Bio::EnsEMBL::AssemblyExceptionFeature();
 my $aef_store2 = new Bio::EnsEMBL::AssemblyExceptionFeature();
 #get ref slice
-my $ref_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome',20);
+my $ref_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome', 6);
 #prepare first object, the haplotype
 $aef_store->start(1500);
 $aef_store->end(35000);