def testFromStringFactorySameTaxa(self): tree_list = datagen.reference_tree_list() tree = dendropy.Tree.get_from_string(tree_list.as_string('nexus'), "nexus", tree_offset=2, taxon_set=tree_list.taxon_set) self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=False)
def testReferenceTreeFileDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream(datagen.reference_trees_filename(schema="nexus")), "nexus") self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None)
def testReferenceTreeFileSameTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-block.nexus"), "nexus", taxon_set=ref_tree_list.taxon_set) self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=False, equal_oids=None)
def testReferenceTreeFileNoTaxaBlockNoTranslateBlockDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-no-translate-block.nexus"), "nexus") self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None)
def testReferenceTreeFileNoTaxaBlockNoTranslateBlockSameTaxa(self): ref_tree_list = datagen.reference_tree_list() reader = dataio.get_reader("nexus", taxon_set=ref_tree_list.taxon_set) dataset = reader.read( stream=pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-no-translate-block.nexus") ) self.assertEqual(len(dataset.tree_lists), 1) self.assertDistinctButEqualTreeList(ref_tree_list, dataset.tree_lists[0], distinct_taxa=False, equal_oids=None)
def testFromFileFactoryDistinctTaxa(self): tree_list = datagen.reference_tree_list() s = pathmap.tree_source_path( datagen.reference_trees_filename(schema="nexus")) tree = dendropy.Tree.get_from_stream(open(s, "rU"), "nexus", tree_offset=2) self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=True)
def testTreeListReaderDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() newick_str = datagen.reference_tree_list_newick_string() t_tree_list = dendropy.TreeList.get_from_string(newick_str, 'newick') self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None, ignore_taxon_order=True)
def testFromPathFactorySameTaxa(self): tree_list = datagen.reference_tree_list() s = pathmap.tree_source_path( datagen.reference_trees_filename(schema="nexus")) tree = dendropy.Tree.get_from_path(s, "nexus", tree_offset=2, taxon_set=tree_list.taxon_set) self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=False)
def testTreeListReaderSameTaxa(self): ref_tree_list = datagen.reference_tree_list() newick_str = datagen.reference_tree_list_newick_string() t_tree_list = dendropy.TreeList.get_from_string(newick_str, 'newick', taxon_set=ref_tree_list.taxon_set) self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=False, equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_path(pathmap.tree_source_path(datagen.reference_trees_filename(schema="newick")), 'newick') self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None, ignore_taxon_order=True)
def testTreeListReaderSameTaxa(self): ref_tree_list = datagen.reference_tree_list() newick_str = datagen.reference_tree_list_newick_string() t_tree_list = dendropy.TreeList.get_from_string( newick_str, 'newick', taxon_set=ref_tree_list.taxon_set) self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=False, equal_oids=None)
def testReferenceTreeFileNoTaxaBlockDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_stream( pathmap.tree_source_stream( "pythonidae.reference-trees.no-taxa-block.nexus"), "nexus") self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_stream( pathmap.tree_source_stream( datagen.reference_trees_filename(schema="nexus")), "nexus") self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None)
def testReferenceTreeFileNoTaxaBlockNoTranslateBlockSameTaxa(self): ref_tree_list = datagen.reference_tree_list() reader = dataio.get_reader('nexus', taxon_set=ref_tree_list.taxon_set) dataset = reader.read(stream=pathmap.tree_source_stream( "pythonidae.reference-trees.no-taxa-no-translate-block.nexus")) self.assertEqual(len(dataset.tree_lists), 1) self.assertDistinctButEqualTreeList(ref_tree_list, dataset.tree_lists[0], distinct_taxa=False, equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() reader = dataio.get_reader('nexus') dataset = reader.read(stream=pathmap.tree_source_stream( datagen.reference_trees_filename(schema="nexus"))) self.assertEqual(len(dataset.tree_lists), 1) self.assertDistinctButEqualTreeList(ref_tree_list, dataset.tree_lists[0], distinct_taxa=True, equal_oids=None)
def testWriteTreeListDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() output_path = pathmap.named_output_path( filename="reference.trees.out.nexus", suffix_timestamp=True) ref_tree_list.write_to_path(output_path, "nexus") t_tree_list = dendropy.TreeList.get_from_path(output_path, "nexus") self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None)
def testReferenceTree(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList() for ref_tree in ref_tree_list: treesplit.encode_splits(ref_tree) splits = ref_tree.split_edges.keys() t_tree = treesplit.tree_from_splits(splits=splits, taxon_set=ref_tree_list.taxon_set, is_rooted=ref_tree.is_rooted) self.assertEqual(ref_tree.symmetric_difference(t_tree), 0)
def testReferenceTreeFileNoTaxaBlockDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() reader = dataio.get_reader('nexus') dataset = reader.read(stream=pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-block.nexus")) self.assertEqual(len(dataset.tree_lists), 1) self.assertDistinctButEqualTreeList( ref_tree_list, dataset.tree_lists[0], distinct_taxa=True, equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() reader = dataio.get_reader('nexus') dataset = reader.read(stream=pathmap.tree_source_stream(datagen.reference_trees_filename(schema="nexus"))) self.assertEqual(len(dataset.tree_lists), 1) self.assertDistinctButEqualTreeList( ref_tree_list, dataset.tree_lists[0], distinct_taxa=True, equal_oids=None)
def testReferenceTree(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList() for ref_tree in ref_tree_list: treesplit.encode_splits(ref_tree) splits = ref_tree.split_edges.keys() t_tree = treesplit.tree_from_splits(splits=splits, taxon_set=ref_tree_list.taxon_set, is_rooted=ref_tree.is_rooted) self.assertEqual(ref_tree.symmetric_difference(t_tree), 0)
def testTreeListReaderDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() newick_str = datagen.reference_tree_list_newick_string() t_tree_list = dendropy.TreeList.get_from_string(newick_str, 'newick') self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None, ignore_taxon_order=True)
def testReferenceTreeFileSameTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_path(pathmap.tree_source_path(datagen.reference_trees_filename(schema="newick")), 'newick', taxon_set=ref_tree_list.taxon_set) self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=False, equal_oids=None)
def testWriteTreeListDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() output_path = pathmap.named_output_path(filename="reference.trees.out.nexus", suffix_timestamp=True) ref_tree_list.write_to_path(output_path, "nexus") t_tree_list = dendropy.TreeList.get_from_path(output_path, "nexus") self.assertDistinctButEqualTreeList( ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_path( pathmap.tree_source_path( datagen.reference_trees_filename(schema="newick")), 'newick') self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=True, equal_oids=None, ignore_taxon_order=True)
def testReferenceTreeFileSameTaxa(self): ref_tree_list = datagen.reference_tree_list() t_tree_list = dendropy.TreeList.get_from_path( pathmap.tree_source_path( datagen.reference_trees_filename(schema="newick")), 'newick', taxon_set=ref_tree_list.taxon_set) self.assertDistinctButEqualTreeList(ref_tree_list, t_tree_list, distinct_taxa=False, equal_oids=None)
def testReferenceTreeList(self): tlist1 = datagen.reference_tree_list() ref_trees_newick = [n.strip() for n in datagen.reference_tree_list_newick_string().split(";")] ref_node_labels = datagen.reference_tree_list_postorder_node_labels() ref_node_rels = datagen.reference_tree_list_node_relationships() for ti, t1 in enumerate(tlist1): t1.assign_node_labels_from_taxon_or_oid() t1_newick = t1.as_newick_string(include_internal_labels=True, preserve_spaces=True) self.assertEqual(t1_newick, ref_trees_newick[ti]) node_labels1 = [nd.label for nd in t1.postorder_node_iter()] self.assertEqual(node_labels1, ref_node_labels[ti]) nodes1 = [nd for nd in t1.postorder_node_iter()] for ndi, nd1 in enumerate(nodes1): ndrel = ref_node_rels[ti][nd1.label] ndrel.test_node(self, nd1)
def testReferenceTreeList(self): tlist1 = datagen.reference_tree_list() ref_trees_newick = [ n.strip() for n in datagen.reference_tree_list_newick_string().split(";") ] ref_node_labels = datagen.reference_tree_list_postorder_node_labels() ref_node_rels = datagen.reference_tree_list_node_relationships() for ti, t1 in enumerate(tlist1): t1.assign_node_labels_from_taxon_or_oid() t1_newick = t1.as_newick_string(include_internal_labels=True, preserve_spaces=True) self.assertEqual(t1_newick, ref_trees_newick[ti]) node_labels1 = [nd.label for nd in t1.postorder_node_iter()] self.assertEqual(node_labels1, ref_node_labels[ti]) nodes1 = [nd for nd in t1.postorder_node_iter()] for ndi, nd1 in enumerate(nodes1): ndrel = ref_node_rels[ti][nd1.label] ndrel.test_node(self, nd1)
def test_b1(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.B1() expected_values = [ 18.686544011544008, 16.862301587301587, 18.012301587301586, 15.803210678210679, 15.803210678210679, 16.219877344877347, 15.80321067821068, 15.80321067821068, 15.803210678210679, 15.80321067821068, 16.10321067821068, ] for idx, tree in enumerate(trees): observed = tree.B1() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_treeness(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.treeness() expected_values = [ 0.82043976304486, 0.30678033634423607, 0.2686940663128338, 0.2674702980152253, 0.2731856127080352, 0.26942308963183575, 0.2764640737121644, 0.26096444220828763, 0.2846852453916621, 0.2791363657987356, 0.28304948441090816, ] for idx, tree in enumerate(trees): observed = tree.treeness() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_b1(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.B1() expected_values = [ 18.686544011544008, 16.862301587301587, 18.012301587301586, 15.803210678210679, 15.803210678210679, 16.219877344877347, 15.80321067821068, 15.80321067821068, 15.803210678210679, 15.80321067821068, 16.10321067821068, ] for idx, tree in enumerate(trees): observed = tree.B1() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_treeness(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.treeness() expected_values = [ 0.82043976304486, 0.30678033634423607, 0.2686940663128338, 0.2674702980152253, 0.2731856127080352, 0.26942308963183575, 0.2764640737121644, 0.26096444220828763, 0.2846852453916621, 0.2791363657987356, 0.28304948441090816, ] for idx, tree in enumerate(trees): observed = tree.treeness() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_gamma2(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.pybus_harvey_gamma() expected_values = [ 6.690070011342222, -2.1016546214332665, -2.2071830302961493, -0.9868763184862083, -1.1223514055125514, -1.0914035287339103, -0.9432772103480326, -0.9855794349340775, -0.7566110136514949, -0.4693672063234924, 0.08314644690264045, ] for idx, tree in enumerate(trees): observed = tree.pybus_harvey_gamma() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_gamma2(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.pybus_harvey_gamma() expected_values = [ 6.690070011342222, -2.1016546214332665, -2.2071830302961493, -0.9868763184862083, -1.1223514055125514, -1.0914035287339103, -0.9432772103480326, -0.9855794349340775, -0.7566110136514949, -0.4693672063234924, 0.08314644690264045, ] for idx, tree in enumerate(trees): observed = tree.pybus_harvey_gamma() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_colless_tree_imbalance(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.colless_tree_imbalance() expected_values = [ 0.3024193548387097, 0.2540322580645161, 0.2762096774193548, 0.3548387096774194, 0.35685483870967744, 0.344758064516129, 0.3548387096774194, 0.35685483870967744, 0.3548387096774194, 0.3548387096774194, 0.3407258064516129, ] for idx, tree in enumerate(trees): observed = tree.colless_tree_imbalance(normalize="max") expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def test_colless_tree_imbalance(self): trees = datagen.reference_tree_list() # for tree in trees: # print tree.colless_tree_imbalance() expected_values = [ 0.3024193548387097, 0.2540322580645161, 0.2762096774193548, 0.3548387096774194, 0.35685483870967744, 0.344758064516129, 0.3548387096774194, 0.35685483870967744, 0.3548387096774194, 0.3548387096774194, 0.3407258064516129, ] for idx, tree in enumerate(trees): observed = tree.colless_tree_imbalance(normalize="max") expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def testNBar(self): trees = datagen.reference_tree_list() # trees = dendropy.TreeList.get_from_path( # src=pathmap.tree_source_path("pythonidae.beast.mcmc.trees"), # schema='nexus') expected_values = [ 7.818181818181818, 7.515151515151516, 7.666666666666667, 8.727272727272727, 8.757575757575758, 8.636363636363637, 8.727272727272727, 8.757575757575758, 8.727272727272727, 8.727272727272727, 8.575757575757576, ] for idx, tree in enumerate(trees): observed = tree.N_bar() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def testNBar(self): trees = datagen.reference_tree_list() # trees = dendropy.TreeList.get_from_path( # src=pathmap.tree_source_path("pythonidae.beast.mcmc.trees"), # schema='nexus') expected_values = [ 7.818181818181818, 7.515151515151516, 7.666666666666667, 8.727272727272727, 8.757575757575758, 8.636363636363637, 8.727272727272727, 8.757575757575758, 8.727272727272727, 8.727272727272727, 8.575757575757576, ] for idx, tree in enumerate(trees): observed = tree.N_bar() expected = expected_values[idx] self.assertAlmostEqual(expected, observed)
def setUp(self): self.trees = datagen.reference_tree_list() self.dna_chars = datagen.reference_dna_matrix() self.std_chars = datagen.reference_standard_matrix()
def setUp(self): reference_tree_list = datagen.reference_tree_list() self.reference_dataset = dendropy.DataSet(reference_tree_list)
def testFromStringFactorySameTaxa(self): tree_list = datagen.reference_tree_list() tree = dendropy.Tree.get_from_string(tree_list.as_string('nexus'), "nexus", tree_offset=2, taxon_set=tree_list.taxon_set) self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=False)
def testFromPathFactorySameTaxa(self): tree_list = datagen.reference_tree_list() s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus")) tree = dendropy.Tree.get_from_path(s, "nexus", tree_offset=2, taxon_set=tree_list.taxon_set) self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=False)
def testFromFileFactoryDistinctTaxa(self): tree_list = datagen.reference_tree_list() s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus")) tree = dendropy.Tree.get_from_stream(open(s, "rU"), "nexus", tree_offset=2) self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=True)
def setUp(self): self.tree_list1 = datagen.reference_tree_list() self.tree_list2 = datagen.reference_tree_list()
def setUp(self): self.tree = reference_tree_list()[0]
def setUp(self): self.tree = reference_tree_list()[0]
def setUp(self): self.trees = datagen.reference_tree_list() self.dna_chars = datagen.reference_dna_matrix() self.std_chars = datagen.reference_standard_matrix()
def setUp(self): reference_tree_list = datagen.reference_tree_list() self.reference_dataset = dendropy.DataSet(reference_tree_list)
def setUp(self): self.ref_tree_list = datagen.reference_tree_list()
def testRoundTreeJustTrees(self): ds = dendropy.DataSet(datagen.reference_tree_list()) self.roundTripDataSetTest(ds, "nexml", ignore_taxon_order=True)
def testFromStringFactoryDistinctTaxa(self): tree_list1 = datagen.reference_tree_list() tree_list2 = dendropy.TreeList.get_from_string(tree_list1.as_string('nexus'), "nexus") self.assertDistinctButEqual(tree_list1, tree_list2, distinct_taxa=True)
def testFromStringFactoryDistinctTaxa(self): tree_list1 = datagen.reference_tree_list() tree_list2 = dendropy.TreeList.get_from_string(tree_list1.as_string('nexus'), "nexus") self.assertDistinctButEqual(tree_list1, tree_list2, distinct_taxa=True)
def setUp(self): self.tree_list1 = datagen.reference_tree_list() self.tree_list1_stream = StringIO(self.tree_list1.as_string("nexus"))
def testFromPathFactoryDistinctTaxa(self): tree_list1 = datagen.reference_tree_list() s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus")) tree_list2 = dendropy.TreeList.get_from_path(s, "nexus") self.assertDistinctButEqual(tree_list1, tree_list2, distinct_taxa=True)
def testRoundTreeJustTrees(self): ds = dendropy.DataSet(datagen.reference_tree_list()) self.roundTripDataSetTest(ds, "nexml", ignore_taxon_order=True)
def setUp(self): self.ref_tree_list = datagen.reference_tree_list()
def setUp(self): self.tree_list1 = datagen.reference_tree_list() self.tree_list1_stream = StringIO(self.tree_list1.as_string("nexus"))
def testFromPathFactoryDistinctTaxa(self): tree_list1 = datagen.reference_tree_list() s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus")) tree_list2 = dendropy.TreeList.get_from_path(s, "nexus") self.assertDistinctButEqual(tree_list1, tree_list2, distinct_taxa=True)
def setUp(self): self.tree_list1 = datagen.reference_tree_list() self.tree_list2 = datagen.reference_tree_list()