included utils BED serialiser testes

modules/t/utils_io/bedSerialiser.t

+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016-2019] 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.
+
+## no critic (RequireFilenameMatchesPackage)
+use strict;
+use warnings;
+
+use Test::More;
+use Test::Warnings;
+use Test::Differences;
+use IO::String;
+
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Utils::IO::BEDSerializer;
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Slice;
+use FindBin qw/$Bin/;
+use Smart::Comments;
+
+my $mtdb = Bio::EnsEMBL::Test::MultiTestDB->new(undef, "$Bin/..");
+my $dba = $mtdb->get_DBAdaptor("core");
+
+# my $nc_db = Bio::EnsEMBL::Test::MultiTestDB->new("circ", "$Bin/..");
+# my $nc_dba = $nc_db->get_DBAdaptor("core");
+
+
+my $id = 'ENSG00000131044';
+my $t_id = 'ENST00000310998'; # or maybe ENST00000278995
+
+my $ga = $dba->get_GeneAdaptor();
+my $ta = $dba->get_TranscriptAdaptor();
+
+{
+  my $gene = $ga->fetch_by_stable_id($id);
+  delete $gene->{source};
+  $gene->{description} = undef; #empty value means don't emit the key
+  my $expected = qq{chr20\t30274333\t30300924\tENSG00000131044\t1000\t+\n};
+
+  assert_bed($gene, $expected, 'Gene with no source serialises to BED as expected. Source is ensembl');
+}
+
+# Test transcripts
+{
+  my $transcript = $ta->fetch_by_stable_id($t_id);
+  my $expected = qq{chr20\t30274333\t30298904\tENST00000310998\t1000\t+\t30274333\t30298904\t0,0,0\t6\t92,112,186,69,74,82,\t0,10117,11263,21390,22172,24489,\tC20orf125\tcmpl\tcmpl\t0,2,0,0,0,2,\tprotein_coding\tENSG00000131044\tC20orf125\tprotein_coding\n};
+  assert_bed($transcript, $expected, 'Transcript emits as genePred format');
+}
+
+# # Uses circ DB core to get a non-coding transcript
+# {
+#   my $nc_ta = $nc_dba->get_TranscriptAdaptor();
+#   my $transcript = $nc_ta->fetch_by_stable_id('BTF1_t31789');
+#   my $expected = qq{chrp02\t155168\t155243\tBTF1_t31789\t1000\t+\t155168\t155168\t0,0,0\t1\t75,\t0,\tBTF1_t31789\tnone\tnone\t0,\ttRNA\tBTF1_t31789\tBTF1_t31789\ttRNA\n};
+#   assert_bed($transcript, $expected, 'Non-coding transcript emits as genePred format');
+# }
+
+{
+  my $sa = $dba->get_SliceAdaptor();
+  my $slice = $sa->fetch_by_region('chromosome', 12, 1, 10);
+  my $feature = Bio::EnsEMBL::Feature->new(
+    -SLICE => $slice,
+    -START => 1,
+    -END => 10,
+    -STRAND => 1,
+  );
+  my $expected = qq{12\t0\t10\t\t1000\t+\n};
+
+  assert_bed($feature, $expected, 'Default feature should seralise without attributes');
+}
+sub assert_bed {
+  my ($feature, $expected, $msg) = @_;
+  my $fh = IO::String->new();
+  my $ser = Bio::EnsEMBL::Utils::IO::BEDSerializer->new($fh);
+  $ser->print_feature($feature);
+  eq_or_diff(${$fh->string_ref()}, $expected, $msg);
+}
+
+done_testing();