Added tests for Gene::get_all_homologous_Genes()

modules/t/MultiTestDB.conf.default

@@ -34,5 +34,8 @@
     'mapping' => {
       'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
     },
+    'multi' => {
+      'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
+    },
   },
 }

modules/t/compara.t

+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016] EMBL-European Bioinformatics Institute
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#      http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+use strict;
+use warnings;
+
+use Test::More;
+use Test::Exception;
+use Data::Dumper;
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
+use Bio::EnsEMBL::Test::TestUtils;
+use Bio::EnsEMBL::Exon;
+use Bio::EnsEMBL::FeaturePair;
+use Bio::EnsEMBL::Transcript;
+use Bio::EnsEMBL::Translation;
+use Bio::EnsEMBL::Gene;
+use Bio::EnsEMBL::DnaDnaAlignFeature;
+
+my $human = Bio::EnsEMBL::Test::MultiTestDB->new('homo_sapiens');
+my $mouse = Bio::EnsEMBL::Test::MultiTestDB->new('mus_musculus');
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new('multi');
+
+my $core_db = $human->get_DBAdaptor('core');
+my $compara_db = $multi->get_DBAdaptor('compara');
+
+
+
+## Gene::get_all_homologous_Genes()
+
+my $human_gene = $core_db->get_GeneAdaptor->fetch_by_stable_id('ENSG00000174852');
+my $homologues = $human_gene->get_all_homologous_Genes();
+is(scalar(@$homologues), 46, 'Got all the homologues');
+
+sub _check_consistency {
+    my $triplet = shift;
+        subtest $triplet->[2], sub {
+            isa_ok($triplet->[0], 'Bio::EnsEMBL::Gene');
+            isa_ok($triplet->[1], 'Bio::EnsEMBL::Compara::Homology');
+            my $members = $triplet->[1]->get_all_Members;
+            is($members->[0]->gene_member->stable_id, 'ENSG00000174852', 'The query gene is correct');
+            is($triplet->[0]->stable_id, $members->[1]->gene_member->stable_id, 'The target gene is consistent between Gene and Homology');
+            is($members->[1]->genome_db->name, $triplet->[2], 'The species name is correct');
+        };
+};
+
+my $mouse_gene = $mouse->get_DBAdaptor('core')->get_GeneAdaptor->fetch_by_stable_id('ENSMUSG00000088524');
+my @mouse_triplets = grep {$_->[2] eq 'mus_musculus'} @$homologues;
+is(scalar(@mouse_triplets), 1, 'One with mouse');
+my $mouse_triplet = $mouse_triplets[0];
+_check_consistency($mouse_triplet);
+subtest 'Mouse triplet', sub {
+    ok($mouse_gene->equals($mouse_triplet->[0]), 'The mouse gene is correct');
+    is($mouse_triplet->[1]->method_link_species_set_id, 50976, 'mouse homology mlss_id');
+    is($mouse_triplet->[1]->dbID, 100972489, 'mouse homology dbID');
+};
+
+# For species with no core database, the Gene object is an empty shell
+my @dog_triplets = grep {$_->[2] eq 'canis_familiaris'} @$homologues;
+is(scalar(@dog_triplets), 1, 'One with dog');
+my $dog_triplet = $dog_triplets[0];
+_check_consistency($dog_triplet);
+subtest 'Dog triplet', sub {
+    ok(!$dog_triplet->[0]->dbID, 'The dog gene is made up and has no dbID');
+    is($dog_triplet->[0]->stable_id, 'ENSCAFG00000027814', 'dog stable_id');
+    is($dog_triplet->[0]->description, 'Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]', 'dog description');
+    is($dog_triplet->[1]->method_link_species_set_id, 50981, 'dog homology mlss_id');
+    is($dog_triplet->[1]->dbID, 100972657, 'dog homology dbID');
+};
+
+
+
+done_testing();

modules/t/test-genome-DBs/multi/compara/dnafrag.txt

+13705552	151834684	5	134	chromosome	1
+4514314	7320470	15	65	chromosome	1
+36722	675822	scaffold_166	4	scaffold	1
+4514338	107808587	Un_random	65	chromosome	1
+2039125	16798506	groupIII	36	group	1
+4346076	202140232	3	60	chromosome	1
+2039164	31848461	17	37	chromosome	1
+1045569	169801366	7	31	chromosome	1
+1045563	189746636	2	31	chromosome	1
+12160504	27241186	9	87	chromosome	1
+2175916	723	Contig213555	43	supercontig	1
+13094385	1346504	GL172955.1	116	scaffold	1
+13200476	158337067	1	122	chromosome	1
+13203820	199944510	3	123	chromosome	1
+12966556	163896628	14	108	chromosome	1
+13049389	1378627	GL343321.1	111	scaffold	1
+13705560	98207768	16	134	chromosome	1
+13636391	3303274	JH126603.1	129	scaffold	1
+13211504	202329955	3	125	chromosome	1
+13785441	2670181	KB743644.1	144	scaffold	1
+13783415	23441680	9	142	chromosome	1
+13688462	12481155	GL831134.1	130	scaffold	1
+13055709	24221871	11	112	chromosome	1
+13705633	42124431	34	135	chromosome	1
+12753243	22517	GeneScaffold_6359	91	genescaffold	1
+13955520	133797422	10	150	chromosome	1
+13862672	17670860	JH603178.1	145	scaffold	1
+14022783	91754291	15	153	chromosome	1
+13203897	11483068	GL873579.1	124	scaffold	1
+13955574	162156779	7	151	chromosome	1
+14026375	59543403	2	154	chromosome	1
+14022801	84932903	24	153	chromosome	1
+13902789	32369425	LG14	148	chromosome	1
+13902799	275612895	1	147	chromosome	1
+3570454	260857928	7	46	chromosome	1
+14018859	2562819	KI519677.1	152	scaffold	1
+13701661	218635234	13	132	chromosome	1
+4346125	59975221	19	61	chromosome	1
+14026979	90463843	11	155	chromosome	1
+13955539	198295559	3	150	chromosome	1
+11302777	39289	GeneScaffold_5302	82	genescaffold	1

modules/t/test-genome-DBs/multi/compara/gene_member.txt

+100000065	ENSTNIG00000020505	0	ENSEMBLGENE	99883	65	100000065	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	4514314	3306094	3306168	1	SNORD2	0	1	1	57	2	0
+100002261	ENSTRUG00000019469	0	ENSEMBLGENE	31033	4	100002260	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	36722	268619	268692	1	SNORD2	0	1	1	58	1	0
+100002264	ENSTRUG00000019394	0	ENSEMBLGENE	31033	4	100002264	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	36722	269022	269095	1	SNORD2	0	1	1	48	1	0
+100003686	ENSTNIG00000020529	0	ENSEMBLGENE	99883	65	100003686	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	4514338	52669397	52669470	-1	SNORD2	0	1	1	48	2	0
+100003687	ENSTNIG00000020519	0	ENSEMBLGENE	99883	65	100003688	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	4514338	52669729	52669803	-1	SNORD2	0	1	1	57	2	0
+100008184	ENSGACG00000022790	0	ENSEMBLGENE	69293	36	100008184	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	2039125	9224992	9225064	1	SNORD2	0	1	1	58	1	0
+100008186	ENSGACG00000022791	0	ENSEMBLGENE	69293	36	100008186	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	2039125	9225550	9225621	1	SNORD2	0	1	1	48	1	0
+100009977	ENSPPYG00000028034	0	ENSEMBLGENE	9601	60	100009977	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	4346076	190574508	190574576	1	SNORD2	0	1	1	45	1	0
+100016849	ENSORLG00000021574	0	ENSEMBLGENE	8090	37	100016849	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	2039164	14653720	14653794	1	SNORD2	0	1	1	58	1	0
+100016850	ENSORLG00000021634	0	ENSEMBLGENE	8090	37	100016850	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	2039164	14654245	14654320	1	SNORD2	0	1	1	48	1	0
+100029371	ENSMMUG00000036232	0	ENSEMBLGENE	9544	31	100029371	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	1045569	164954481	164954549	1	SNORD2	0	1	1	33	3	0
+100033919	ENSMMUG00000037192	0	ENSEMBLGENE	9544	31	100033919	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	1045563	179142348	179142416	1	SNORD2	0	1	1	44	3	0
+100046335	ENSTGUG00000018017	0	ENSEMBLGENE	59729	87	100046335	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	12160504	18582628	18582698	1	SNORD2	0	1	1	58	0	0
+100047101	ENSOANG00000027382	0	ENSEMBLGENE	9258	43	100047100	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	2175916	513	593	-1	SNORD2	0	1	1	58	0	0
+100054945	ENSXETG00000029617	0	ENSEMBLGENE	8364	116	100054945	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13094385	381059	381128	-1	SNORD2	0	1	1	49	1	0
+100054946	ENSXETG00000029793	0	ENSEMBLGENE	8364	116	100054946	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13094385	385005	385076	-1	SNORD2	0	1	1	58	1	0
+100065013	ENSBTAG00000044311	0	ENSEMBLGENE	9913	122	100065013	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13200476	81062767	81062835	-1	SNORD2	0	1	1	47	0	0
+100071636	ENSGGOG00000032407	0	ENSEMBLGENE	9595	123	100071636	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13203820	188240400	188240468	1	SNORD2	0	1	1	45	1	0
+100087720	ENSOCUG00000023265	0	ENSEMBLGENE	9986	108	100088181	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	12966556	78843854	78843921	-1	SNORD2	0	1	1	45	2	0
+100093454	ENSACAG00000018292	0	ENSEMBLGENE	28377	111	100094079	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13049389	118621	118692	-1	SNORD2	0	1	1	58	0	0
+100099604	ENSMUSG00000088524	0	ENSEMBLGENE	10090	134	100100368	small nucleolar RNA, C/D box 2 [Source:MGI Symbol;Acc:MGI:3819528]	13705560	23108953	23109021	1	Snord2	0	1	1	45	0	0
+100099742	ENSLACG00000021456	0	ENSEMBLGENE	7897	129	100100505	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13636391	2411690	2411759	1	SNORD2	0	1	1	49	0	0
+100113582	ENSPTRG00000037854	0	ENSEMBLGENE	9598	125	100114678	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13211504	190852362	190852430	1	SNORD2	0	1	1	45	1	0
+100123418	ENSAPLG00000000068	0	ENSEMBLGENE	8839	144	100124975	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13785441	276440	276510	1	SNORD2	0	1	1	58	0	0
+100130549	ENSGALG00000025617	0	ENSEMBLGENE	9031	142	100132105	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13783415	15672950	15673019	1	SNORD2	0	1	1	58	0	0
+100137301	ENSONIG00000022215	0	ENSEMBLGENE	8128	130	100138857	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13688462	12140155	12140229	1	SNORD2	0	1	1	58	1	0
+100137304	ENSONIG00000022099	0	ENSEMBLGENE	8128	130	100138860	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13688462	12140712	12140786	1	SNORD2	0	1	1	48	1	0
+100151878	ENSMGAG00000000091	0	ENSEMBLGENE	9103	112	100153475	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13055709	16212140	16212209	1	SNORD2	0	1	1	58	0	0
+100162160	ENSCAFG00000027814	0	ENSEMBLGENE	9615	135	100164038	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13705633	19356118	19356186	1	SNORD2	0	1	1	45	5	0
+100164895	ENSMEUG00000017324	0	ENSEMBLGENE	9315	91	100166821	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	12753243	17043	17112	1	SNORD2	0	1	1	58	0	0
+100176264	ENSG00000238707	0	ENSEMBLGENE	9606	150	100178494	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13955520	56595963	56596031	-1	SNORD2	0	1	1	45	1	0
+100182621	ENSFALG00000015549	0	ENSEMBLGENE	59894	145	100185036	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13862672	11103001	11103071	1	SNORD2	0	1	1	58	0	0
+100184508	ENSCSAG00000026646	0	ENSEMBLGENE	60711	153	100186963	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14022783	81076307	81076375	1	SNORD2	0	1	1	44	2	0
+100191757	ENSOGAG00000023959	0	ENSEMBLGENE	30611	124	100194492	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13203897	9863584	9863651	-1	SNORD2	0	1	1	45	0	0
+100204308	ENSPANG00000010082	0	ENSEMBLGENE	9555	151	100207705	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13955574	157844257	157844325	1	SNORD2	0	1	1	45	1	0
+100215815	ENSDARG00000082639	0	ENSEMBLGENE	7955	154	100220003	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14026375	7922554	7922624	1	SNORD2	0	1	1	48	2	0
+100215819	ENSDARG00000083056	0	ENSEMBLGENE	7955	154	100220007	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14026375	7922934	7923004	1	SNORD2	0	1	1	42	2	0
+100215833	ENSDARG00000080523	0	ENSEMBLGENE	7955	154	100220025	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14026375	7925865	7925936	1	SNORD2	0	1	1	58	2	0
+100220485	ENSCSAG00000027032	0	ENSEMBLGENE	60711	153	100225049	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14022801	79602435	79602503	1	SNORD2	0	1	1	33	2	0
+100223263	ENSLOCG00000019102	0	ENSEMBLGENE	7918	148	100227949	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13902789	461949	462018	1	SNORD2	0	1	1	58	0	0
+100226195	ENSOARG00000022667	0	ENSEMBLGENE	9940	147	100231022	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13902799	198671751	198671819	-1	SNORD2	0	1	1	47	1	0
+100235573	ENSMODG00000026826	0	ENSEMBLGENE	13616	46	100240803	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	3570454	206772418	206772486	-1	SNORD2	0	1	1	58	0	0
+100238959	ENSPFOG00000021602	0	ENSEMBLGENE	48698	152	100244296	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14018859	380507	380583	1	SNORD2	0	1	1	58	1	0
+100238967	ENSPFOG00000021430	0	ENSEMBLGENE	48698	152	100244304	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14018859	381062	381137	1	SNORD2	0	1	1	48	1	0
+100242730	ENSSSCG00000018746	0	ENSEMBLGENE	9823	132	100248134	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	13701661	133974703	133974771	1	SNORD2	0	1	1	45	2	0
+100246488	ENSECAG00000027514	0	ENSEMBLGENE	9796	61	100252028	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	4346125	24791922	24791988	1	SNORD2	0	1	1	45	1	0
+100263700	ENSRNOG00000053621	0	ENSEMBLGENE	10116	155	100270056	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	14026979	81378396	81378464	-1	SNORD2	0	1	1	45	0	0
+100277999	ENSG00000174852	0	ENSEMBLGENE	9606	150	100285954	small nucleolar RNA, C/D box 2 [Source:HGNC Symbol;Acc:HGNC:32678]	13955539	186784796	186784864	1	SNORD2	0	1	1	45	1	0
+100281324	ENSTSYG00000021671	0	ENSEMBLGENE	9478	82	100289437	Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299]	11302777	17893	17961	1	SNORD2	0	1	1	45	0	0