Tests for RegulatoryFeatureAdaptor.pm

modules/t/regulatoryFeatureAdaptor.t

+use strict;
+use Bio::EnsEMBL::Test::TestUtils;
+
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+
+BEGIN { $| = 1;
+	use Test;
+	plan tests => 13;
+}
+
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
+my $db = $multi_db->get_DBAdaptor('core');
+
+my $verbose = 0;
+
+# Test Creation
+
+my $rfa = $db->get_RegulatoryFeatureAdaptor();
+
+ok(ref($rfa) && $rfa->isa('Bio::EnsEMBL::DBSQL::RegulatoryFeatureAdaptor'));
+
+#
+## retrieve a feature via dbID
+#
+debug('---- fetch_by_dbID (default coords) ----');
+my $feat = $rfa->fetch_by_dbID(2);
+ok($feat->dbID == 2);
+ok($feat->slice->seq_region_name() eq '3');
+ok($feat->start == 49546683);
+ok($feat->end == 49546702);
+ok($feat->strand == 1);
+
+# test fetch all by motif
+my $rma = $db->get_RegulatoryMotifAdaptor();
+my $motif = $rma->fetch_by_name('motif1');
+ok($motif);
+ok(@{$rfa->fetch_all_by_motif($motif)} == 10);
+
+# List_dbidx
+my $ids = $rfa->list_dbIDs();
+ok (@{$ids});
+
+
+# Test store
+
+$multi_db->save('core', 'regulatory_feature');
+
+my $slice = $db->get_SliceAdaptor()->fetch_by_seq_region_id(469286);
+
+my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name('miRanda');
+
+my $rm = Bio::EnsEMBL::RegulatoryMotif->new(-name => 'motif1',
+					    -type => 'miRNA_target');
+
+my $rf = Bio::EnsEMBL::RegulatoryFeature->new(-name      => 'hsa-miR-108',
+					      -start     => 100,
+					      -end       => 220,
+					      -strand    => -1,
+					      -slice     => $slice,
+					      -analysis  => $analysis,
+					      -motif     => $motif,
+					      -influence => 'positive',
+					      -adaptor   => $rfa);
+
+$rfa->store($rf);
+
+ok($rf->dbID && $rf->adaptor());
+
+$rf = $rfa->fetch_by_dbID($rf->dbID());
+
+ok($rf->name()  eq 'hsa-miR-108');
+ok($rf->start() eq 100);
+ok($rf->analysis()->logic_name() eq 'miRanda');
+
+$multi_db->restore('core', 'regulatory_feature');