Python tree_source_stream Examples

Example #1

File: test_dataio_newick.py Project: nesnidal/DendroPy

 def testBasicDocumentFromInit(self):
     test_dataset = dendropy.DataSet(stream=pathmap.tree_source_stream(
         datagen.reference_trees_filename(schema="newick")),
                                     schema="newick")
     self.assertDistinctButEqual(self.reference_dataset,
                                 test_dataset,
                                 ignore_taxon_order=True)

Example #2

File: test_dataio_newick.py Project: nesnidal/DendroPy

 def testBasicDocumentParseFromReader(self):
     reader = newick.NewickReader()
     test_dataset = reader.read(stream=pathmap.tree_source_stream(
         datagen.reference_trees_filename(schema="newick")))
     self.assertDistinctButEqual(self.reference_dataset,
                                 test_dataset,
                                 ignore_taxon_order=True)

Example #3

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 #4

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 #5

 def testNexusDistinctTaxa(self):
     stream = pathmap.tree_source_stream(
         datagen.reference_trees_filename(schema="nexus"))
     for idx, test_tree in enumerate(
             dataio.tree_source_iter(stream=stream, schema='nexus/newick')):
         self.assertDistinctButEqualTree(self.ref_tree_list[idx],
                                         test_tree,
                                         distinct_taxa=True)

Example #6

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 #7

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 #8

 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 #9

 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 #10

File: test_num_lineages_through_time.py Project: gregcaporaso/DendroPy

 def test_ultrametric(self):
     trees = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.nexus"), "nexus")
     for tree in trees:
         dists = tree.calc_node_root_distances()
         min_dist, max_dist = tree.minmax_leaf_distance_from_root()
         trunc_dists = [(max_dist * f) for f in (0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9)]
         for td in trunc_dists:
             num_lineages = tree.num_lineages_at(td)
             self.check_tree(tree, td, num_lineages)

Example #11

 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 #12

 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 #13

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 #14

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 #15

File: test_num_lineages_through_time.py Project: wrightaprilm/DendroPy

 def test_ultrametric(self):
     trees = dendropy.TreeList.get_from_stream(
         pathmap.tree_source_stream("pythonidae.reference-trees.nexus"),
         "nexus")
     for tree in trees:
         dists = tree.calc_node_root_distances()
         min_dist, max_dist = tree.minmax_leaf_distance_from_root()
         trunc_dists = [(max_dist * f) for f in (0.1, 0.2, 0.3, 0.4, 0.5,
                                                 0.6, 0.7, 0.8, 0.9)]
         for td in trunc_dists:
             num_lineages = tree.num_lineages_at(td)
             self.check_tree(tree, td, num_lineages)

Example #16

File: test_tree_truncation.py Project: gregcaporaso/DendroPy

 def setUp(self):
     self.trees = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.nexus"), "nexus")

Example #17

File: test_dataio_nexus.py Project: jjhoyt/gengis

 def testNewickSameTaxa(self):
     stream = pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick"))
     for idx, test_tree in enumerate(dataio.tree_source_iter(stream=stream, schema='nexus/newick', taxon_set=self.ref_tree_list.taxon_set)):
         self.assertDistinctButEqualTree(self.ref_tree_list[idx], test_tree, distinct_taxa=False)

Example #18

File: test_dataio_nexus.py Project: jjhoyt/gengis

 def testNewickDistinctTaxa(self):
     stream = pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick"))
     for idx, test_tree in enumerate(dataio.tree_source_iter(stream=stream, schema='nexus/newick')):
         self.assertDistinctButEqualTree(self.ref_tree_list[idx], test_tree, distinct_taxa=True, ignore_taxon_order=True)

Example #19

File: generate_reference_tree.py Project: BioinformaticsArchive/DendroPy

def main():
    tlist = dendropy.TreeList(stream=pathmap.tree_source_stream(datagen.reference_trees_filename("nexus")), schema="nexus")
    for idx, t in enumerate(tlist):
        t.label = "Tree%02d" % (idx+1)
        t.assign_node_labels_from_taxon_or_oid()

    result = []

    result.append("def reference_tree_list_postorder_node_labels():")
    result.append("    return [")
    for t in tlist:
        nodes = [("'" + nd.label + "'") for nd in t.postorder_node_iter()]
        result.append("        [%s]," % (",".join(nodes)))
    result.append("    ]")
    result.append("")

    result.append("def reference_tree_list_newick_string(taxon_set=None):")
    result.append('    return """\\')
    for t in tlist:
        result.append('        %s;' % t.as_newick_string(include_internal_labels=True))
    result.append('    """')
    result.append("")

    result.append("def reference_tree_list_node_relationships():")
    result.append("    treelist_node_references = [")
    for t in tlist:
        result.append("        {")
        for nd in t:
            if nd.parent_node is not None:
                pn_label = "'" + nd.parent_node.label + "'"
            else:
                pn_label = 'None'
            if nd.taxon is not None:
                t_label = "'" + nd.taxon.label + "'"
            else:
                t_label = 'None'
            result.append("            '%s' : NodeRelationship(parent_label=%s, child_labels=[%s], edge_length=%s, taxon_label=%s)," % \
                (nd.label,
                 pn_label,
                 ",".join(["'"+c.label+"'" for c in nd.child_nodes()]),
                 nd.edge.length,
                 t_label))
        result.append("        },")
    result.append("    ]")
    result.append("    return treelist_node_references")
    result.append("")

    tree_list_name = 'tree_list'
    src_lines = tlist.as_python_source(tree_list_name=tree_list_name, oids=True).split("\n")
    result.append("def reference_tree_list(taxon_set=None):")
    src_lines[0] = re.sub("(dendropy\.TreeList\(label\=.*)\)", "\g<1>, taxon_set=taxon_set)", src_lines[0])
    for s in src_lines:
        result.append("    %s" % s)
    result.append("""\

    # set labels of nodes with taxa to taxon label, else oid (for consistent
    # identification in debugging)
    for t in %s:
        t.assign_node_labels_from_taxon_or_oid()

    return %s
    """ % (tree_list_name, tree_list_name))
    result.append("")

    sys.stdout.write("\n".join(result))

Example #20

File: test_dataobject_cloning.py Project: emilhaegglund/wgfast

 def setUp(self):
     s = pathmap.tree_source_stream("pythonidae.annotated.nexml")
     self.dataset = dendropy.DataSet.get_from_stream(s, "nexml")

Example #21

 def testReadSummaryTree(self):
     tree = dendropy.Tree.get_from_stream(pathmap.tree_source_stream('pythonidae.beast.summary.tre'), 'beast-summary-tree')
     self.verify_node_info(tree)

Example #22

File: test_dataio_newick.py Project: jjhoyt/gengis

 def testBasicDocumentFromInit(self):
     test_dataset = dendropy.DataSet(stream=pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick")), schema="newick")
     self.assertDistinctButEqual(self.reference_dataset, test_dataset, ignore_taxon_order=True)

Example #23

File: test_dataio_newick.py Project: jjhoyt/gengis

 def testBasicDocumentParseFromReader(self):
     reader = newick.NewickReader()
     test_dataset = reader.read(stream=pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick")))
     self.assertDistinctButEqual(self.reference_dataset, test_dataset, ignore_taxon_order=True)

Example #24

 def setUp(self):
     self.trees = dendropy.TreeList.get_from_stream(
         pathmap.tree_source_stream("pythonidae.reference-trees.nexus"),
         "nexus")

Example #25

File: test_annotations.py Project: BioinformaticsArchive/DendroPy

 def testParseNexmlAnnotations(self):
     s = pathmap.tree_source_stream("treebase_s373.xml")
     dataset = dendropy.DataSet(stream=s, schema="nexml")
     self.verify_dataset(dataset)

Example #26

 def testSummaryTreeIter(self):
     stream = pathmap.tree_source_stream('pythonidae.beast.summary.tre')
     for tree in dendropy.tree_source_iter(stream, 'beast-summary-tree'):
         self.verify_node_info(tree)

Example #27

 def testParseNexmlAnnotations(self):
     s = pathmap.tree_source_stream("treebase_s373.xml")
     dataset = dendropy.DataSet(stream=s, schema="nexml")
     self.verify_dataset(dataset)

Example #28

def main():
    tlist = dendropy.TreeList(stream=pathmap.tree_source_stream(
        datagen.reference_trees_filename("nexus")),
                              schema="nexus")
    for idx, t in enumerate(tlist):
        t.label = "Tree%02d" % (idx + 1)
        t.assign_node_labels_from_taxon_or_oid()

    result = []

    result.append("def reference_tree_list_postorder_node_labels():")
    result.append("    return [")
    for t in tlist:
        nodes = [("'" + nd.label + "'") for nd in t.postorder_node_iter()]
        result.append("        [%s]," % (",".join(nodes)))
    result.append("    ]")
    result.append("")

    result.append("def reference_tree_list_newick_string(taxon_set=None):")
    result.append('    return """\\')
    for t in tlist:
        result.append('        %s;' %
                      t.as_newick_string(include_internal_labels=True))
    result.append('    """')
    result.append("")

    result.append("def reference_tree_list_node_relationships():")
    result.append("    treelist_node_references = [")
    for t in tlist:
        result.append("        {")
        for nd in t:
            if nd.parent_node is not None:
                pn_label = "'" + nd.parent_node.label + "'"
            else:
                pn_label = 'None'
            if nd.taxon is not None:
                t_label = "'" + nd.taxon.label + "'"
            else:
                t_label = 'None'
            result.append("            '%s' : NodeRelationship(parent_label=%s, child_labels=[%s], edge_length=%s, taxon_label=%s)," % \
                (nd.label,
                 pn_label,
                 ",".join(["'"+c.label+"'" for c in nd.child_nodes()]),
                 nd.edge.length,
                 t_label))
        result.append("        },")
    result.append("    ]")
    result.append("    return treelist_node_references")
    result.append("")

    tree_list_name = 'tree_list'
    src_lines = tlist.as_python_source(tree_list_name=tree_list_name,
                                       oids=True).split("\n")
    result.append("def reference_tree_list(taxon_set=None):")
    src_lines[0] = re.sub("(dendropy\.TreeList\(label\=.*)\)",
                          "\g<1>, taxon_set=taxon_set)", src_lines[0])
    for s in src_lines:
        result.append("    %s" % s)
    result.append("""\

    # set labels of nodes with taxa to taxon label, else oid (for consistent
    # identification in debugging)
    for t in %s:
        t.assign_node_labels_from_taxon_or_oid()

    return %s
    """ % (tree_list_name, tree_list_name))
    result.append("")

    sys.stdout.write("\n".join(result))