def test_buildtreemap_one_line(self, mock_annotation, mock_tree, mock_root):
mock_annotation.return_value = mock.Mock(gene_name='mock_gene')
mock_root.return_value = mock.Mock(gene_name='mock_gene', annotations=[])
mock_lines = self._format_filedata(['line1'])
with mock.patch("builtins.open", mock_open(read_data=mock_lines)):
result = annotate.build_tree_map(['mock_file_path'])
self.assertEqual(len(result.keys()), 1)
def test_buildtreemap_no_duplicate_chromosomes(self, mock_annotation, mock_tree):
anno_1 = mock.Mock(gene_name='mock_gene', chromosome='chr1')
anno_2 = mock.Mock(gene_name='mock_gene2', chromosome='chr2')
mock_annotation.side_effect = [anno_1, anno_2]
mock_lines = self._format_filedata(['line1', 'line2'])
with mock.patch("builtins.open", mock_open(read_data=mock_lines)):
result = annotate.build_tree_map(['mock_file_path'])
self.assertEqual(len(result.keys()), 2)
def test_buildtreemap_root_has_right_node(self):
dir_path = os.path.dirname(os.path.realpath(__file__))
fixture_path = "../../fixtures/gtf/hg19_fixture3.gtf"
fixture_path = os.path.join(dir_path, fixture_path)
tree_map = annotate.build_tree_map(fixture_path)
self.assertEqual(tree_map['chr3'].start, 38589553)
self.assertEqual(tree_map['chr3'].end, 38691164)
self.assertEqual(tree_map['chr3'].right_node.start, 134196546)
self.assertEqual(tree_map['chr3'].right_node.end, 134204866)
def test_buildtreemap_map_has_two_entries(self):
dir_path = os.path.dirname(os.path.realpath(__file__))
fixture_path = "../../fixtures/gtf/hg19_fixture1.gtf"
fixture_path = os.path.join(dir_path, fixture_path)
tree_map = annotate.build_tree_map(fixture_path)
self.assertEqual(tree_map['chr3'].start, 134196546)
self.assertEqual(tree_map['chr3'].end, 134204866)
self.assertEqual(tree_map['chr9'].start, 136325087)
self.assertEqual(tree_map['chr9'].end, 136335910)
def test_buildtreemap_empty_file(self, mock_annotation, mock_root):
with mock.patch("builtins.open", mock_open(read_data="")):
result = annotate.build_tree_map(['mock_file_path'])
self.assertEqual(result, {})