updated test cases to check integrity of api once deprecated tables, columns...

updated test cases to check integrity of api once deprecated tables, columns and methods have been removed
test databases patched to schema 74

modules/t/canonicalDBAdaptor.t

@@ -23,10 +23,6 @@ $test_adaptor = $db->get_ArchiveStableIdAdaptor();
 if (defined $test_adaptor) {
   ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor"));
 }
-$test_adaptor = $db->get_QtlFeatureAdaptor();
-ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor"));
-$test_adaptor = $db->get_QtlAdaptor();
-ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlAdaptor"));
 $test_adaptor = $db->get_ProteinFeatureAdaptor();
 ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor"));
 $test_adaptor = $db->get_PredictionTranscriptAdaptor();

modules/t/dnaAlignFeatureAdaptor.t

@@ -56,7 +56,6 @@ ok($feat);
 print_features([$feat]);
 ok($feat->db_name eq 'EMBL');
 ok($feat->db_display_name eq 'EMBL');
-ok($feat->pair_dna_align_feature_id == 1449321);
 
 
 $feat = $feat->transform('supercontig');
@@ -96,7 +95,6 @@ my $evalue     = 23.2;
 my $cigar_string = '100M';
 my $hcoverage  = 99.5;
 my $external_db_id = 2200;
-my $pair_dna_align_feature_id = 10;
 
 $feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
   (-START  => $start,
@@ -113,8 +111,7 @@ $feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
    -P_VALUE => $evalue,
    -ANALYSIS => $analysis,
    -HCOVERAGE => $hcoverage,
-   -EXTERNAL_DB_ID => $external_db_id,
-   -PAIR_DNA_ALIGN_FEATURE_ID => $pair_dna_align_feature_id );
+   -EXTERNAL_DB_ID => $external_db_id);
 
 ok(!$feat->is_stored($db));
 
@@ -142,7 +139,6 @@ ok($feat->p_value == $evalue);
 ok($feat->analysis->logic_name eq $analysis->logic_name);
 ok($feat->external_db_id == $external_db_id);
 ok($feat->hcoverage == $hcoverage);
-ok($feat->pair_dna_align_feature_id == $pair_dna_align_feature_id);
 
 $multi->restore('core', 'dna_align_feature');
 
@@ -166,4 +162,4 @@ sub print_features {
   }
 }
 
-done_testing();
\ No newline at end of file
+done_testing();

modules/t/gene.t

@@ -766,47 +766,6 @@ ok($gene->is_current == 1);
 
 $multi->restore;
 
-#
-# Tests for unconventional transcript association functionality
-#
-
-# test a gene with existing associations
-$gene = $ga->fetch_by_dbID(18256);
-ok(@{$gene->get_all_unconventional_transcript_associations()} == 3);
-
-# test removing them all
-$gene->remove_unconventional_transcript_associations();
-ok(@{$gene->get_all_unconventional_transcript_associations()} == 0);
-
-# test adding to a new gene
-my $new_gene       = $ga->fetch_by_dbID(18260);
-my $new_transcript = $db->get_TranscriptAdaptor()->fetch_by_dbID(21720);
-
-ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 0);
-$new_gene->add_unconventional_transcript_association($new_transcript, 'sense_intronic');
-ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 1);
-
-# test storing
-
-$new_gene = $ga->fetch_by_dbID(18261);
-ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 0);
-
-$new_gene->add_unconventional_transcript_association($new_transcript, 'sense_intronic');
-$new_gene->add_unconventional_transcript_association($new_transcript, 'antisense');
-
-$ga->store($new_gene);
-
-# test removing
-$new_gene->remove_unconventional_transcript_associations();
-
-my $utaa = $db->get_UnconventionalTranscriptAssociationAdaptor();
-ok(@{$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
-
 #test the get_species_and_object_type method from the Registry
 my $registry = 'Bio::EnsEMBL::Registry';
 my ($species, $object_type, $db_type) = $registry->get_species_and_object_type('ENSG00000355555');
@@ -814,7 +773,7 @@ ok($species eq 'homo_sapiens' && $object_type eq 'Gene');
 
 # Testing compara dba retrieval
 {
-  dies_ok { $new_gene->get_all_homologous_Genes(); } 'No Compara DBAdaptor has been configured. No way to retrieve data';
+  dies_ok { $gene->get_all_homologous_Genes(); } 'No Compara DBAdaptor has been configured. No way to retrieve data';
 }
 
 done_testing();

modules/t/objectLoad.t

@@ -26,7 +26,6 @@ my $expected_keys = {
     is_current biotype status source
     description
     canonical_transcript canonical_transcript_id _transcript_array
-    canonical_annotation
     dbentries display_xref external_name external_db external_status
   /],
   'transcript' => [sort @generic_keys, @location_keys, qw/
@@ -85,4 +84,4 @@ sub assert_keys {
 
 sub get_keys {
   return [sort keys %{$_[0]}];
-}
\ No newline at end of file
+}

modules/t/qtl.t

-use strict;
-use warnings;
-use Test::More;
-
-use Bio::EnsEMBL::Test::MultiTestDB;
-use Bio::EnsEMBL::Map::Marker;
-use Bio::EnsEMBL::Map::MarkerSynonym;
-
-use Bio::EnsEMBL::Map::DBSQL::QtlAdaptor;
-use Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor;
-use Bio::EnsEMBL::Slice;
-
-use Bio::EnsEMBL::Test::TestUtils;
-
-our $verbose = 0; #set to 1 to turn on debug printouts
-
-my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
-my $db = $multi->get_DBAdaptor( 'core' );
-my $sa = $db->get_SliceAdaptor();
-
-
-
-my $slice = $sa->fetch_by_region( 'chromosome', "20" );
-
-my $qtl_features = $slice->get_all_QtlFeatures();
-
-debug( "found ".scalar( @$qtl_features ) );
-debug( join( "\n", map { "$_" } %{$qtl_features->[0]})."\n" );
-debug( join( "\n", map { "$_" } %{$qtl_features->[1]})."\n" );
-
-ok( scalar( @$qtl_features ) == 2 );
-
-my $qtladptor = $db->get_QtlAdaptor();
-my $traits = $qtladptor->list_traits();
-
-
-debug( join( "\n", map {"Trait: $_"} @$traits ));
-ok( scalar( @$traits ) == 2 );
-
-my $qtls = $qtladptor->fetch_all_by_trait( $traits->[0] );
-my $qf = $qtls->[0]->get_QtlFeature();
-
-debug( join( "\n", %$qf ));
-ok( $qf->isa( "Bio::EnsEMBL::Map::QtlFeature" ));
-
-my $qtl = $qtls->[0];
-ok($qtl->flank_marker_1->isa('Bio::EnsEMBL::Map::Marker'));
-ok($qtl->flank_marker_2->isa('Bio::EnsEMBL::Map::Marker'));
-
-my $synonyms = $qtl->get_synonyms;
-
-ok($synonyms->{'rat genome database'} eq 'rqtl2');
-
-done_testing();

modules/t/test-genome-DBs/circ/core/meta.txt

@@ -3,8 +3,13 @@
 58	\N	patch	patch_72_73_a.sql|schema_version
 59	\N	patch	patch_72_73_b.sql|alt_allele_type
 60	\N	patch	patch_72_73_c.sql|add_object_type_marker
+62	\N	patch	patch_73_74_a.sql|schema_version
+63	\N	patch	patch_73_74_c.sql|remove_unconventional_transcript_association
+64	\N	patch	patch_73_74_d.sql|remove_qtl
+65	\N	patch	patch_73_74_e.sql|remove_canonical_annotation
+66	\N	patch	patch_73_74_f.sql|remove_pair_dna_align
 1	\N	schema_type	core
-2	\N	schema_version	73
+2	\N	schema_version	74
 8	1	assembly.accession	GCA_000292705.1
 10	1	assembly.date	2012-08
 7	1	assembly.default	GCA_000292705.1
@@ -21,6 +26,7 @@
 16	1	genebuild.method	Generated from ENA annotation
 13	1	genebuild.start_date	2012-08-EnsemblBacteria
 12	1	genebuild.version	2012-08-EnsemblBacteria
+61	1	patch	patch_73_74_b.sql|remove_dnac
 42	1	provider.name	European Nucleotide Archive
 43	1	provider.url	http://www.ebi.ac.uk/ena/data/view/GCA_000292705
 18	1	repeat.analysis	Dust
@@ -45,8 +51,8 @@
 21	1	species.classification	Bacillus thuringiensis
 20	1	species.classification	Bacillus thuringiensis HD-789
 28	1	species.classification	Bacteria
-27	1	species.classification	Firmicutes
 29	1	species.classification	cellular organisms
+27	1	species.classification	Firmicutes
 34	1	species.common_name	Bacillus thuringiensis HD-789
 39	1	species.db_name	bacillus_thuringiensis
 33	1	species.display_name	Bacillus thuringiensis HD-789

modules/t/test-genome-DBs/circ/core/table.sql

@@ -102,7 +102,7 @@ CREATE TABLE `attrib_type` (
   `description` text,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB AUTO_INCREMENT=14078 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=391 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -142,7 +142,7 @@ CREATE TABLE `density_feature` (
   PRIMARY KEY (`density_feature_id`),
   KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
   KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=1051 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 
 CREATE TABLE `density_type` (
   `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -152,7 +152,7 @@ CREATE TABLE `density_type` (
   `value_type` enum('sum','ratio') NOT NULL,
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -216,14 +216,12 @@ CREATE TABLE `dna_align_feature` (
   `external_db_id` int(10) unsigned DEFAULT NULL,
   `hcoverage` double DEFAULT NULL,
   `external_data` text,
-  `pair_dna_align_feature_id` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`dna_align_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
   KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `external_db_idx` (`external_db_id`),
-  KEY `pair_idx` (`pair_dna_align_feature_id`)
+  KEY `external_db_idx` (`external_db_id`)
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `exon` (
@@ -290,7 +288,6 @@ CREATE TABLE `gene` (
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
-  `canonical_annotation` varchar(255) DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
   `version` smallint(5) unsigned NOT NULL DEFAULT '1',
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
@@ -454,11 +451,11 @@ CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
   `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+  `meta_value` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=InnoDB AUTO_INCREMENT=61 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=67 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -649,37 +646,6 @@ CREATE TABLE `protein_feature` (
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=InnoDB AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1;
 
-CREATE TABLE `qtl` (
-  `qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `trait` varchar(255) NOT NULL,
-  `lod_score` float DEFAULT NULL,
-  `flank_marker_id_1` int(10) unsigned DEFAULT NULL,
-  `flank_marker_id_2` int(10) unsigned DEFAULT NULL,
-  `peak_marker_id` int(10) unsigned DEFAULT NULL,
-  PRIMARY KEY (`qtl_id`),
-  KEY `trait_idx` (`trait`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
-CREATE TABLE `qtl_feature` (
-  `seq_region_id` int(10) unsigned NOT NULL,
-  `seq_region_start` int(10) unsigned NOT NULL,
-  `seq_region_end` int(10) unsigned NOT NULL,
-  `qtl_id` int(10) unsigned NOT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
-  KEY `qtl_idx` (`qtl_id`),
-  KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
-  KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
-CREATE TABLE `qtl_synonym` (
-  `qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `qtl_id` int(10) unsigned NOT NULL,
-  `source_database` enum('rat genome database','ratmap') NOT NULL,
-  `source_primary_id` varchar(255) NOT NULL,
-  PRIMARY KEY (`qtl_synonym_id`),
-  KEY `qtl_idx` (`qtl_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `repeat_name` varchar(255) NOT NULL,
@@ -718,7 +684,7 @@ CREATE TABLE `seq_region` (
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
   KEY `cs_idx` (`coord_system_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=14 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -744,7 +710,7 @@ CREATE TABLE `seq_region_synonym` (
   PRIMARY KEY (`seq_region_synonym_id`),
   UNIQUE KEY `syn_idx` (`synonym`),
   KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -897,14 +863,6 @@ CREATE TABLE `translation_attrib` (
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 
-CREATE TABLE `unconventional_transcript_association` (
-  `transcript_id` int(10) unsigned NOT NULL,
-  `gene_id` int(10) unsigned NOT NULL,
-  `interaction_type` enum('antisense','sense_intronic','sense_overlaping_exonic','chimeric_sense_exonic') DEFAULT NULL,
-  KEY `transcript_idx` (`transcript_id`),
-  KEY `gene_idx` (`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `type` enum('xref','cDNA','Marker') NOT NULL,

modules/t/test-genome-DBs/homo_sapiens/core/gene.txt

-18256	protein_coding	1282	469283	30274334	30300924	1	152202	ensembl	KNOWN	DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474, ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL;Acc:Q9BR18]	1	21716	longest transcript in gene	ENSG00000131044	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18257	protein_coding	1282	469283	30301733	30318881	1	0	ensembl	NOVEL	\N	1	21718	\N	ENSG00000174873	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18258	protein_coding	1282	469283	30320853	30327869	-1	40090	vega	KNOWN	\N	1	21719	\N	ENSG00000088356	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18259	protein_coding	1282	469283	30371004	30372906	1	102413	ensembl	KNOWN	DJ310O13.4 (NOVEL PROTEIN SIMILAR TO PREDICTED C. ELEGANS AND C. INTESTINALIS PROTEINS) (FRAGMENT). [Source:SPTREMBL;Acc:Q9NUG5]	1	21720	\N	ENSG00000101321	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18260	protein_coding	1282	469283	30386305	30408041	1	34986	vega	KNOWN	\N	1	21721	\N	ENSG00000101331	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18261	protein_coding	1282	469283	30428114	30477716	1	158525	ensembl	KNOWN	TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK AND P60-HCK) (HEMOPOIETIC CELL KINASE). [Source:SWISSPROT;Acc:P08631]	1	21723	\N	ENSG00000101336	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18262	protein_coding	1282	469283	30485596	30543114	1	120576	ensembl	KNOWN	TRANSMEMBRANE 9 SUPERFAMILY PROTEIN MEMBER 4. [Source:SWISSPROT;Acc:Q92544]	1	21724	\N	ENSG00000101337	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18263	protein_coding	1282	469283	30565065	30566129	-1	128607	ensembl	KNOWN	BA392M18.1 (NOVEL PROTEIN SIMILAR TO TESTIS SPECIFIC PROTEIN TSPY). [Source:SPTREMBL;Acc:Q9H489]	1	21725	\N	ENSG00000125979	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18264	protein_coding	1282	469283	30568364	30583588	-1	17034	ensembl	KNOWN	ZINC FINGER PROTEIN PLAGL2 (PLEIOMORPHIC ADENOMA-LIKE PROTEIN 2). [Source:SWISSPROT;Acc:Q9UPG8]	1	21726	\N	ENSG00000126003	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18265	protein_coding	1282	469283	30583753	30614524	1	128597	ensembl	KNOWN	GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 PRECURSOR (EC 2.4.1.-) (O- FUCOSYLTRANSFERASE) (O-FUCT-1). [Source:SPTREMBL;Acc:Q9H488]	1	21728	\N	ENSG00000101346	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18266	protein_coding	1282	469283	30653524	30709209	1	28819	ensembl	KNOWN	KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [Source:SWISSPROT;Acc:O15066]	1	21729	1	ENSG00000101350	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18267	protein_coding	1282	469283	30735607	30815178	1	128324	ensembl	KNOWN	BA358N2.1 (KIAA0978) (FRAGMENT). [Source:SPTREMBL;Acc:Q9H466]	1	21731	\N	ENSG00000171456	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18268	protein_coding	1282	469283	30822726	30859269	-1	34892	ensembl	KNOWN	\N	1	21732	\N	ENSG00000125964	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18269	protein_coding	1282	469283	30885729	30911383	-1	89323	ensembl	KNOWN	DJ1184F4.4 (NOVEL PROTEIN SIMILAR TO NUCLEOLAR PROTEIN 4 (NOL4) (NOLP)). [Source:SPTREMBL;Acc:Q9NQF5]	1	21734	\N	ENSG00000088303	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18270	protein_coding	1282	469283	31070930	31071301	-1	332	ensembl	KNOWN	\N	1	21735	\N	ENSG00000174852	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18271	protein_coding	1282	469283	31074431	31089984	-1	168324	ensembl	KNOWN	\N	1	21736	\N	ENSG00000149600	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18272	protein_coding	1282	469283	31108924	31155894	1	15966	ensembl	KNOWN	DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B (EC 2.1.1.37) (DNMT3B) (DNA METHYLTRANSFERASE HSAIIIB) (DNA MTASE HSAIIIB) (M.HSAIIIB). [Source:SWISSPROT;Acc:Q9UBC3]	1	21737	\N	ENSG00000088305	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18273	protein_coding	1282	469283	31166507	31196939	1	97759	ensembl	KNOWN	MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691]	1	21738	\N	ENSG00000101367	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18274	protein_coding	1282	469283	31210077	31225346	1	0	ensembl	NOVEL	\N	1	21739	\N	ENSG00000167097	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18275	protein_coding	1282	965899	10060	10405	1	0	ensembl	NOVEL	\N	1	21740	\N	ENSG00000355555	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18256	protein_coding	1282	469283	30274334	30300924	1	152202	ensembl	KNOWN	DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474, ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL;Acc:Q9BR18]	1	21716	ENSG00000131044	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18257	protein_coding	1282	469283	30301733	30318881	1	0	ensembl	NOVEL	\N	1	21718	ENSG00000174873	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18258	protein_coding	1282	469283	30320853	30327869	-1	40090	vega	KNOWN	\N	1	21719	ENSG00000088356	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18259	protein_coding	1282	469283	30371004	30372906	1	102413	ensembl	KNOWN	DJ310O13.4 (NOVEL PROTEIN SIMILAR TO PREDICTED C. ELEGANS AND C. INTESTINALIS PROTEINS) (FRAGMENT). [Source:SPTREMBL;Acc:Q9NUG5]	1	21720	ENSG00000101321	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18260	protein_coding	1282	469283	30386305	30408041	1	34986	vega	KNOWN	\N	1	21721	ENSG00000101331	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18261	protein_coding	1282	469283	30428114	30477716	1	158525	ensembl	KNOWN	TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK AND P60-HCK) (HEMOPOIETIC CELL KINASE). [Source:SWISSPROT;Acc:P08631]	1	21723	ENSG00000101336	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18262	protein_coding	1282	469283	30485596	30543114	1	120576	ensembl	KNOWN	TRANSMEMBRANE 9 SUPERFAMILY PROTEIN MEMBER 4. [Source:SWISSPROT;Acc:Q92544]	1	21724	ENSG00000101337	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18263	protein_coding	1282	469283	30565065	30566129	-1	128607	ensembl	KNOWN	BA392M18.1 (NOVEL PROTEIN SIMILAR TO TESTIS SPECIFIC PROTEIN TSPY). [Source:SPTREMBL;Acc:Q9H489]	1	21725	ENSG00000125979	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18264	protein_coding	1282	469283	30568364	30583588	-1	17034	ensembl	KNOWN	ZINC FINGER PROTEIN PLAGL2 (PLEIOMORPHIC ADENOMA-LIKE PROTEIN 2). [Source:SWISSPROT;Acc:Q9UPG8]	1	21726	ENSG00000126003	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18265	protein_coding	1282	469283	30583753	30614524	1	128597	ensembl	KNOWN	GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 PRECURSOR (EC 2.4.1.-) (O- FUCOSYLTRANSFERASE) (O-FUCT-1). [Source:SPTREMBL;Acc:Q9H488]	1	21728	ENSG00000101346	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18266	protein_coding	1282	469283	30653524	30709209	1	28819	ensembl	KNOWN	KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [Source:SWISSPROT;Acc:O15066]	1	21729	ENSG00000101350	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18267	protein_coding	1282	469283	30735607	30815178	1	128324	ensembl	KNOWN	BA358N2.1 (KIAA0978) (FRAGMENT). [Source:SPTREMBL;Acc:Q9H466]	1	21731	ENSG00000171456	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18268	protein_coding	1282	469283	30822726	30859269	-1	34892	ensembl	KNOWN	\N	1	21732	ENSG00000125964	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18269	protein_coding	1282	469283	30885729	30911383	-1	89323	ensembl	KNOWN	DJ1184F4.4 (NOVEL PROTEIN SIMILAR TO NUCLEOLAR PROTEIN 4 (NOL4) (NOLP)). [Source:SPTREMBL;Acc:Q9NQF5]	1	21734	ENSG00000088303	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18270	protein_coding	1282	469283	31070930	31071301	-1	332	ensembl	KNOWN	\N	1	21735	ENSG00000174852	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18271	protein_coding	1282	469283	31074431	31089984	-1	168324	ensembl	KNOWN	\N	1	21736	ENSG00000149600	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18272	protein_coding	1282	469283	31108924	31155894	1	15966	ensembl	KNOWN	DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B (EC 2.1.1.37) (DNMT3B) (DNA METHYLTRANSFERASE HSAIIIB) (DNA MTASE HSAIIIB) (M.HSAIIIB). [Source:SWISSPROT;Acc:Q9UBC3]	1	21737	ENSG00000088305	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18273	protein_coding	1282	469283	31166507	31196939	1	97759	ensembl	KNOWN	MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691]	1	21738	ENSG00000101367	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18274	protein_coding	1282	469283	31210077	31225346	1	0	ensembl	NOVEL	\N	1	21739	ENSG00000167097	1	2004-12-06 12:00:00	2004-12-06 12:00:00
+18275	protein_coding	1282	965899	10060	10405	1	0	ensembl	NOVEL	\N	1	21740	ENSG00000355555	1	2004-12-06 12:00:00	2004-12-06 12:00:00

modules/t/test-genome-DBs/homo_sapiens/core/meta.txt

-1	\N	schema_version	73
+1	\N	schema_version	74
 2	1	assembly.default	NCBI34
-33	1	species.classification	Chordata
-32	1	species.classification	Vertebrata
-31	1	species.classification	Mammalia
-30	1	species.classification	Eutheria
-29	1	species.classification	Primates
-28	1	species.classification	Catarrhini
+3	1	species.taxonomy_id	9606
+26	1	species.classification	Homo sapiens
 27	1	species.classification	Hominidae
+28	1	species.classification	Catarrhini
+29	1	species.classification	Primates
+30	1	species.classification	Eutheria
+31	1	species.classification	Mammalia
+32	1	species.classification	Vertebrata
+33	1	species.classification	Chordata
 34	1	species.classification	Metazoa
 35	1	species.classification	Eukaryota
-26	1	species.classification	Homo sapiens
 36	1	species.common_name	Human
-70	1	species.scientific_name	Homo sapiens
-3	1	species.taxonomy_id	9606
 55	1	assembly.mapping	chromosome:NCBI33|contig
 56	1	assembly.mapping	clone|contig
 57	1	assembly.mapping	supercontig|contig
@@ -23,6 +22,7 @@
 65	1	assembly.mapping	alt_chrom#chromosome:NCBI33
 66	1	assembly.mapping	alt_chrom|chromosome:NCBI33|contig
 67	1	species.production_name	homo_sapiens
+70	1	species.scientific_name	Homo sapiens
 71	\N	patch	patch_68_69_a.sql|schema_version
 72	\N	patch	patch_69_70_a.sql|schema_version
 73	\N	patch	patch_69_70_b.sql|add_mapping_set_history
@@ -37,3 +37,9 @@
 82	\N	patch	patch_72_73_a.sql|schema_version
 83	\N	patch	patch_72_73_b.sql|alt_allele_type
 84	\N	patch	patch_72_73_c.sql|add_object_type_marker
+85	\N	patch	patch_73_74_b.sql|remove_dnac
+88	\N	patch	patch_73_74_a.sql|schema_version
+89	\N	patch	patch_73_74_c.sql|remove_unconventional_transcript_association
+90	\N	patch	patch_73_74_d.sql|remove_qtl
+97	\N	patch	patch_73_74_e.sql|remove_canonical_annotation
+98	\N	patch	patch_73_74_f.sql|remove_pair_dna_align

modules/t/test-genome-DBs/homo_sapiens/core/qtl.txt

-1	stupidity	-0.2	20	92	94
-2	long nose	-0.1	20	65	66

modules/t/test-genome-DBs/homo_sapiens/core/qtl_feature.txt

-469283	30100000	30400000	1	10
-469283	30268968	31005297	2	10

modules/t/test-genome-DBs/homo_sapiens/core/qtl_synonym.txt

-1	1	rat genome database	rqtl1
-2	1	ratmap	rmqtl1
-3	2	rat genome database	rqtl2

modules/t/test-genome-DBs/homo_sapiens/core/unconventional_transcript_association.txt

-21716	18256	antisense
-21717	18256	antisense
-21719	18256	sense_intronic
-21718	18257	sense_intronic
-21718	18258	antisense