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Commit 77ab0df7 authored by Glenn Proctor's avatar Glenn Proctor
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Tweaks

parent 5ba1a210
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......@@ -26,18 +26,18 @@ ok(ref($rfa) && $rfa->isa('Bio::EnsEMBL::DBSQL::RegulatoryFeatureAdaptor'));
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->slice->seq_region_name() eq '1');
ok($feat->start == 919787);
ok($feat->end == 919807);
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);
# test fetch all by factor
my $rma = $db->get_RegulatoryFactorAdaptor();
my $factor = $rma->fetch_by_name('hsa-miR-138');
ok($factor);
ok(@{$rfa->fetch_all_by_factor($factor)} == 2);
# List_dbidx
# List_dbids
my $ids = $rfa->list_dbIDs();
ok (@{$ids});
......@@ -53,7 +53,7 @@ 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',
my $rm = Bio::EnsEMBL::RegulatoryFactor->new(-name => 'factor1',
-type => 'miRNA_target');
my $rf = Bio::EnsEMBL::RegulatoryFeature->new(-name => 'hsa-miR-108',
......@@ -62,8 +62,7 @@ my $rf = Bio::EnsEMBL::RegulatoryFeature->new(-name => 'hsa-miR-108',
-strand => -1,
-slice => $slice,
-analysis => $analysis,
-motif => $motif,
-influence => 'positive',
-factor => $factor,
-adaptor => $rfa);
$rfa->store($rf);
......
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