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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
import dendropy
import collections
from dendropy.test.support import curated_test_tree
from dendropy.test.support import standard_file_test_chars
class StandardSingleTaxonNamespaceDataSet(curated_test_tree.CuratedTestTree):
@staticmethod
def build(cls):
standard_file_test_chars.DnaTestChecker.build()
standard_file_test_chars.RnaTestChecker.build()
standard_file_test_chars.ProteinTestChecker.build()
standard_file_test_chars.Standard01234TestChecker.build()
def verify_chars(self, ds):
self.assertEqual(len(ds.taxon_namespaces), 1)
tns = ds.taxon_namespaces[0]
checkers = (
standard_file_test_chars.RnaTestChecker,
standard_file_test_chars.ProteinTestChecker,
standard_file_test_chars.Standard01234TestChecker,
standard_file_test_chars.DnaTestChecker,
)
self.assertEqual(len(ds.char_matrices), len(checkers))
for idx, (char_matrix, checker) in enumerate(zip(ds.char_matrices, checkers)):
self.assertIs(char_matrix.taxon_namespace, tns)
if checker.matrix_type is dendropy.StandardCharacterMatrix:
checker.create_class_fixtures_label_sequence_map_based_on_state_alphabet(checker,
char_matrix.default_state_alphabet)
standard_file_test_chars.general_char_matrix_checker(
self,
char_matrix,
checker,
check_taxon_annotations=self.check_taxon_annotations,
check_matrix_annotations=self.check_matrix_annotations,
check_sequence_annotations=self.check_sequence_annotations,
check_column_annotations=self.check_column_annotations,
check_cell_annotations=self.check_cell_annotations,)
def verify_trees(self, ds):
self.assertEqual(len(ds.taxon_namespaces), 1)
tns = ds.taxon_namespaces[0]
self.assertEqual(len(ds.tree_lists), 7)
for tree_list_idx, tree_list in enumerate(ds.tree_lists):
self.assertIs(tree_list.taxon_namespace, tns)
expected_labels = (
'the first tree',
'the SECOND tree',
'The Third Tree',
)
self.assertEqual(len(tree_list), len(expected_labels))
for tree_idx, (tree, expected_label) in enumerate(zip(tree_list, expected_labels)):
# print(tree_list_idx, tree_idx)
self.assertEqual(tree.label, expected_label)
self.verify_curated_tree(
tree=tree,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False,
suppress_edge_lengths=False,
node_taxon_label_map=None)
def verify_dataset(self, ds):
self.verify_chars(ds)
self.verify_trees(ds)
class MultipleTaxonNamespaceDataSet(object):
expected_taxa = collections.OrderedDict()
expected_taxa["X1"] = ("x1.1", "x1.2", "x1.3", "x1.4", "x1.5", )
expected_taxa["X2"] = ("x2.1", "x2.2", "x2.3", "x2.4", )
expected_taxa["X3"] = ("x3.1", "x3.2", "x3.3", "x3.4", "x3.5", "x3.6", )
expected_chars = collections.OrderedDict()
expected_chars["X1"] = ("x1.chars1", "x1.chars2", "x1.chars3", )
expected_chars["X2"] = ("x2.chars1", "x2.chars2")
expected_trees = collections.OrderedDict()
expected_trees["X1"] = ("x1.trees1", "x1.trees3", "x1.trees3",)
expected_trees["X2"] = ("x2.trees1", "x2.trees2")
def verify_attached_taxon_namespace_written(self, ds, taxon_namespace):
self.assertEqual(len(ds.taxon_namespaces), 1)
expected_tns_label = taxon_namespace.label
# self.assertEqual(ds.taxon_namespaces[0].label, expected_tns_label)
expected_tlsts = MultipleTaxonNamespaceDataSet.expected_trees.get(expected_tns_label, [])
self.assertEqual(len(ds.char_matrices), len(expected_tlsts))
expected_cms = MultipleTaxonNamespaceDataSet.expected_chars.get(expected_tns_label, [])
self.assertEqual(len(ds.tree_lists), len(expected_cms))
def verify_attached_taxon_namespace(self, ds, attached_taxon_namespace):
self.assertEqual(len(ds.taxon_namespaces), 1)
self.assertIs(ds.taxon_namespaces[0], attached_taxon_namespace)
self.assertEqual(len(ds.taxon_namespaces[0]),
sum(len(v) for v in MultipleTaxonNamespaceDataSet.expected_taxa.values()))
self.assertEqual(len(ds.char_matrices),
sum(len(v) for v in MultipleTaxonNamespaceDataSet.expected_chars.values()))
self.assertEqual(len(ds.tree_lists),
sum(len(v) for v in MultipleTaxonNamespaceDataSet.expected_trees.values()))
for block in (ds.tree_lists, ds.char_matrices):
for item in block:
self.assertIs(item.taxon_namespace, attached_taxon_namespace)
if hasattr(item[0], "taxon_namespace"):
for subitem in item:
self.assertIs(subitem.taxon_namespace, attached_taxon_namespace)
def verify_unrestricted(self, ds):
self.assertEqual(len(ds.taxon_namespaces), len(MultipleTaxonNamespaceDataSet.expected_taxa))
self.assertEqual(len(ds.char_matrices),
sum(len(v) for v in MultipleTaxonNamespaceDataSet.expected_chars.values()))
self.assertEqual(len(ds.tree_lists),
sum(len(v) for v in MultipleTaxonNamespaceDataSet.expected_trees.values()))
for tns, expected_tns_label in zip(ds.taxon_namespaces, MultipleTaxonNamespaceDataSet.expected_taxa):
self.assertEqual(tns.label, expected_tns_label)
expected_tns = MultipleTaxonNamespaceDataSet.expected_taxa[expected_tns_label]
self.assertEqual(len(tns), len(expected_tns))
for taxon, expected_label in zip(tns, expected_tns):
self.assertEqual(taxon.label, expected_label)
cms = [char_matrix for char_matrix in ds.char_matrices if char_matrix.taxon_namespace is tns]
expected_cms = MultipleTaxonNamespaceDataSet.expected_chars.get(expected_tns_label, [])
self.assertEqual(len(cms), len(expected_cms))
tlst = [tree_list for tree_list in ds.tree_lists if tree_list.taxon_namespace is tns]
expected_tlsts = MultipleTaxonNamespaceDataSet.expected_trees.get(expected_tns_label, [])
self.assertEqual(len(tlst), len(expected_tlsts))
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