Python reference_tree_list Examples

Example #1

 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)

Example #2

File: test_dataio_nexus.py Project: jjhoyt/gengis

 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)

Example #3

File: test_dataio_nexus.py Project: jjhoyt/gengis

 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)

Example #4

File: test_dataio_nexus.py Project: jjhoyt/gengis

 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)

Example #5

File: test_dataio_nexus.py Project: BioinformaticsArchive/wgfast

 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)

Example #6

 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)

Example #7

File: test_dataio_newick.py Project: nesnidal/DendroPy

 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)

Example #8

 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)

Example #9

File: test_dataio_newick.py Project: jjhoyt/gengis

 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)

Example #10

File: test_dataio_newick.py Project: jjhoyt/gengis

 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)

Example #11

File: test_dataio_newick.py Project: nesnidal/DendroPy

 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)

Example #12

 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)

Example #13

 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)

Example #14

 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)

Example #15

 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)

Example #16

 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)

Example #17

File: test_tree_from_splits.py Project: wrightaprilm/DendroPy

 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)

Example #18

File: test_dataio_nexus.py Project: jjhoyt/gengis

 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)

Example #19

File: test_dataio_nexus.py Project: jjhoyt/gengis

 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)

Example #20

File: test_tree_from_splits.py Project: jjhoyt/gengis

 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)

Example #21

File: test_dataio_newick.py Project: jjhoyt/gengis

 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)

Example #22

File: test_dataio_newick.py Project: jjhoyt/gengis

 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)

Example #23

File: test_dataio_nexus.py Project: jjhoyt/gengis

 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)

Example #24

File: test_dataio_newick.py Project: nesnidal/DendroPy

 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)

Example #25

File: test_dataio_newick.py Project: nesnidal/DendroPy

 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)

Example #26

File: test_datagen.py Project: BioinformaticsArchive/DendroPy

 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)

Example #27

File: test_datagen.py Project: nesnidal/DendroPy

 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)

Example #28

File: test_tree_metrics.py Project: gregcaporaso/DendroPy

 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)

Example #29

File: test_tree_metrics.py Project: gregcaporaso/DendroPy

 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)

Example #30

File: test_tree_metrics.py Project: wrightaprilm/DendroPy

 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)

Example #31

File: test_tree_metrics.py Project: wrightaprilm/DendroPy

 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)

Example #32

File: test_tree_metrics.py Project: wrightaprilm/DendroPy

 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)

Example #33

File: test_tree_metrics.py Project: gregcaporaso/DendroPy

 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)

Example #34

File: test_tree_metrics.py Project: wrightaprilm/DendroPy

 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)

Example #35

File: test_tree_metrics.py Project: gregcaporaso/DendroPy

 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)

Example #36

File: test_tree_metrics.py Project: wrightaprilm/DendroPy

 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)

Example #37

File: test_tree_metrics.py Project: gregcaporaso/DendroPy

 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)

Example #38

File: test_ape.py Project: jjhoyt/gengis

 def setUp(self):
     self.trees = datagen.reference_tree_list()
     self.dna_chars = datagen.reference_dna_matrix()
     self.std_chars = datagen.reference_standard_matrix()

Example #39

File: test_dataio_newick.py Project: jjhoyt/gengis

 def setUp(self):
     reference_tree_list = datagen.reference_tree_list()
     self.reference_dataset = dendropy.DataSet(reference_tree_list)

Example #40

File: test_dataobject_tree.py Project: BioinformaticsArchive/DendroPy

 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)

Example #41

File: test_dataobject_tree.py Project: BioinformaticsArchive/DendroPy

 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)

Example #42

File: test_dataobject_tree.py Project: BioinformaticsArchive/DendroPy

 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)

Example #43

File: test_tree_metrics.py Project: emilhaegglund/wgfast

 def setUp(self):
     self.tree_list1 = datagen.reference_tree_list()
     self.tree_list2 = datagen.reference_tree_list()

Example #44

File: test_asciitree.py Project: emilhaegglund/wgfast

 def setUp(self):
     self.tree = reference_tree_list()[0]

Example #45

File: test_asciitree.py Project: BioinformaticsArchive/DendroPy

 def setUp(self):
     self.tree = reference_tree_list()[0]

Example #46

File: test_ape.py Project: emilhaegglund/wgfast

 def setUp(self):
     self.trees = datagen.reference_tree_list()
     self.dna_chars = datagen.reference_dna_matrix()
     self.std_chars = datagen.reference_standard_matrix()

Example #47

File: test_dataio_newick.py Project: nesnidal/DendroPy

 def setUp(self):
     reference_tree_list = datagen.reference_tree_list()
     self.reference_dataset = dendropy.DataSet(reference_tree_list)

Example #48

File: test_dataio_newick.py Project: nesnidal/DendroPy

 def setUp(self):
     self.ref_tree_list = datagen.reference_tree_list()

Example #49

File: test_dataio_nexml.py Project: BioinformaticsArchive/DendroPy

 def testRoundTreeJustTrees(self):
     ds = dendropy.DataSet(datagen.reference_tree_list())
     self.roundTripDataSetTest(ds, "nexml", ignore_taxon_order=True)

Example #50

File: test_dataobject_tree_list.py Project: BioinformaticsArchive/DendroPy

 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)

Example #51

File: test_dataobject_tree_list.py Project: nesnidal/DendroPy

 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)

Example #52

File: test_dataobject_tree_list.py Project: BioinformaticsArchive/DendroPy

 def setUp(self):
     self.tree_list1 = datagen.reference_tree_list()
     self.tree_list1_stream = StringIO(self.tree_list1.as_string("nexus"))

Example #53

File: test_dataobject_tree_list.py Project: nesnidal/DendroPy

 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)

Example #54

 def testRoundTreeJustTrees(self):
     ds = dendropy.DataSet(datagen.reference_tree_list())
     self.roundTripDataSetTest(ds, "nexml", ignore_taxon_order=True)

Example #55

File: test_dataio_nexus.py Project: jjhoyt/gengis

 def setUp(self):
     self.ref_tree_list = datagen.reference_tree_list()

Example #56

File: test_dataobject_tree_list.py Project: nesnidal/DendroPy

 def setUp(self):
     self.tree_list1 = datagen.reference_tree_list()
     self.tree_list1_stream = StringIO(self.tree_list1.as_string("nexus"))

Example #57

File: test_dataobject_tree_list.py Project: BioinformaticsArchive/DendroPy

 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)

Example #58

File: test_tree_metrics.py Project: BioinformaticsArchive/DendroPy

 def setUp(self):
     self.tree_list1 = datagen.reference_tree_list()
     self.tree_list2 = datagen.reference_tree_list()