Added tests for biotype

modules/t/biotype.t

+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016-2018] 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::Warnings qw( allow_warnings );
+use Test::Exception;
+
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
+
+our $verbose = 0; #set to 1 to turn on debug printouts
+
+
+
+# Get a DBAdaptor to from the test system
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
+ok($multi);
+my $db = $multi->get_DBAdaptor("core");
+ok($db);
+
+# Should get meaningful type back
+debug("get biotype adaptor");
+my $biotype_adaptor = $db->get_BiotypeAdaptor();
+ok($biotype_adaptor->isa("Bio::EnsEMBL::DBSQL::BiotypeAdaptor"));
+
+# fetch a protein_coding gene object
+debug("fetch gene");
+my $ga = $db->get_GeneAdaptor();
+my $gene = $ga->fetch_by_stable_id("ENSG00000171456");
+ok($gene);
+
+# test biotype related methods on this gene object
+debug("gene biotype");
+is($gene->{'biotype'}, 'protein_coding');
+is($gene->biotype, 'protein_coding');
+
+# test gene biotype object
+my $biotype = $gene->biotype;
+ok($biotype->isa("Bio::EnsEMBL::Biotype"));
+is($biotype->object_type, 'gene', 'Biotype is from Gene object');
+is($biotype->name, 'protein_coding', 'Biotype name is protein_coding');
+is($biotype->biotype_group, 'coding', 'Biotype group is coding');
+is($biotype->so_acc, 'SO:0001217', 'Biotype protein_coding refers to SO:0001217');
+throws_ok { $biotype->so_acc('test') } qr/so_acc must be a Sequence Ontology accession/,  'so_acc() requires a SO acc like string';
+throws_ok { $biotype->object_type('test') } qr/object_type must be gene or transcript/,  'object_type() must be gene or transcript';
+
+# test transcript biotype object
+my $transcript = $gene->canonical_transcript;
+debug("transcript biotype");
+is($transcript->{'biotype'}, 'protein_coding');
+is($transcript->biotype, 'protein_coding');
+$biotype = $transcript->biotype;
+ok($biotype->isa("Bio::EnsEMBL::Biotype"));
+is($biotype->object_type, 'transcript', 'Biotype is from Transcript object');
+is($biotype->name, 'protein_coding', 'Biotype name is protein_coding');
+is($biotype->biotype_group, 'coding', 'Biotype group is coding');
+is($biotype->so_acc, 'SO:0000234', 'Biotype protein_coding refers to SO:0000234');
+
+# test fetch biotypes of object_type gene
+my $biotypes = $biotype_adaptor->fetch_all_by_object_type('gene');
+is(ref $biotypes, 'ARRAY', 'got an array');
+is(scalar @{$biotypes}, '2', 'of size 2');
+
+done_testing();

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

+64	protein_coding	gene	core,otherfeatures,rnaseq,vega,presite	\N	\N	coding	SO:0001217
+65	protein_coding	transcript	core,otherfeatures,rnaseq,vega,presite	\N	\N	coding	SO:0000234
+87	tRNA	gene	core,otherfeatures,presite	76	\N	snoncoding	SO:0001263
+