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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.
##
##############################################################################
"""
Tests basic DataSet curation
"""
import collections
import unittest
import dendropy
from dendropy.test.support import dendropytest
from dendropy.test.support import curated_test_tree_list
from dendropy.test.support import standard_file_test_chars
class EmptyDataSetWithLabelCreationTestCase(dendropytest.ExtendedTestCase):
def test_basic_create_with_label(self):
ds = dendropy.DataSet(label="d1")
self.assertEqual(ds.label, "d1")
class DataSetAddTestCase(dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_chars.DnaTestChecker.build()
standard_file_test_chars.ProteinTestChecker.build()
def setUp(self):
self.expected_taxon_namespaces = []
self.standalone_taxon_namespaces = []
self.standalone_taxon_namespaces.append(dendropy.TaxonNamespace(["t1", "t2", "t3"]))
self.standalone_taxon_namespaces.append(dendropy.TaxonNamespace(["s1", "s2", "s3"]))
self.expected_taxon_namespaces.extend(self.standalone_taxon_namespaces)
self.expected_tree_lists = collections.OrderedDict()
for i in range(2):
pdo1 = curated_test_tree_list.get_tree_list(4)
self.expected_tree_lists[pdo1] = pdo1.taxon_namespace
self.expected_taxon_namespaces.append(pdo1.taxon_namespace)
for j in range(2):
pdo2 = curated_test_tree_list.get_tree_list(4,
taxon_namespace=pdo1.taxon_namespace)
self.expected_tree_lists[pdo2] = pdo2.taxon_namespace
self.expected_char_matrices = collections.OrderedDict()
for i in range(2):
pdo1 = standard_file_test_chars.DnaTestChecker.get_char_matrix_from_class_data()
self.expected_char_matrices[pdo1] = pdo1.taxon_namespace
self.expected_taxon_namespaces.append(pdo1.taxon_namespace)
for j in range(2):
pdo2 = standard_file_test_chars.ProteinTestChecker.get_char_matrix_from_class_data(taxon_namespace=pdo1.taxon_namespace)
self.expected_char_matrices[pdo2] = pdo2.taxon_namespace
def test_basic_add_taxon_namespace(self):
expected_fundamental_states = set()
ds = dendropy.DataSet()
for tns in self.expected_taxon_namespaces:
ds.add_taxon_namespace(tns)
self.assertEqual(len(ds.taxon_namespaces), len(self.expected_taxon_namespaces))
for x1, x2 in zip(ds.taxon_namespaces, self.expected_taxon_namespaces):
self.assertIs(x1, x2)
def test_basic_add_tree_list(self):
ds = dendropy.DataSet()
expected_taxon_namespaces = collections.OrderedDict()
for tree_list in self.expected_tree_lists:
ds.add_tree_list(tree_list)
expected_taxon_namespaces[self.expected_tree_lists[tree_list]] = True
self.assertEqual(len(ds.taxon_namespaces), len(expected_taxon_namespaces))
for x1, x2 in zip(ds.taxon_namespaces, expected_taxon_namespaces):
self.assertIs(x1, x2)
self.assertEqual(len(ds.tree_lists), len(self.expected_tree_lists))
for x1, x2 in zip(ds.tree_lists, self.expected_tree_lists):
self.assertIs(x1, x2)
self.assertIs(x1.taxon_namespace, self.expected_tree_lists[x1])
for t in x1:
self.assertIs(t.taxon_namespace, x1.taxon_namespace)
def test_basic_add_char_matrix(self):
ds = dendropy.DataSet()
expected_taxon_namespaces = collections.OrderedDict()
for char_matrix in self.expected_char_matrices:
ds.add_char_matrix(char_matrix)
expected_taxon_namespaces[self.expected_char_matrices[char_matrix]] = True
self.assertEqual(len(ds.taxon_namespaces), len(expected_taxon_namespaces))
for x1, x2 in zip(ds.taxon_namespaces, expected_taxon_namespaces):
self.assertIs(x1, x2)
self.assertEqual(len(ds.char_matrices), len(self.expected_char_matrices))
for x1, x2 in zip(ds.char_matrices, self.expected_char_matrices):
self.assertIs(x1, x2)
self.assertIs(x1.taxon_namespace, self.expected_char_matrices[x1])
def test_basic_add(self):
ds = dendropy.DataSet()
for tns in self.standalone_taxon_namespaces:
ds.add(tns)
for tree_list in self.expected_tree_lists:
ds.add(tree_list)
for char_matrix in self.expected_char_matrices:
ds.add(char_matrix)
self.assertEqual(len(ds.taxon_namespaces), len(self.expected_taxon_namespaces))
for x1, x2 in zip(ds.taxon_namespaces, self.expected_taxon_namespaces):
self.assertIs(x1, x2)
for x1, x2 in zip(ds.tree_lists, self.expected_tree_lists):
self.assertIs(x1, x2)
for x1, x2 in zip(ds.char_matrices, self.expected_char_matrices):
self.assertIs(x1, x2)
def test_construction(self):
item_list = []
item_list.extend(self.standalone_taxon_namespaces)
item_list.extend(self.expected_tree_lists)
item_list.extend(self.expected_char_matrices)
ds = dendropy.DataSet(item_list)
self.assertEqual(len(ds.taxon_namespaces), len(self.expected_taxon_namespaces))
for x1, x2 in zip(ds.taxon_namespaces, self.expected_taxon_namespaces):
self.assertIs(x1, x2)
for x1, x2 in zip(ds.tree_lists, self.expected_tree_lists):
self.assertIs(x1, x2)
for x1, x2 in zip(ds.char_matrices, self.expected_char_matrices):
self.assertIs(x1, x2)
class DataSetNewTestCase(dendropytest.ExtendedTestCase):
def test_basic_new_taxon_namespace(self):
ds = dendropy.DataSet()
tax_labels = ["a", "b", "c", "d", "e"]
tns_labels = ["t1", "t2", "t3"]
tns_list = []
for tns_label in tns_labels:
tns = ds.new_taxon_namespace(tax_labels, label=tns_label)
self.assertTrue(isinstance(tns, dendropy.TaxonNamespace))
tns_list.append(tns)
self.assertEqual(len(tns_list), len(tns_labels))
for tns, tns_label in zip(tns_list, tns_labels):
self.assertEqual(tns.label, tns_label)
self.assertEqual(len(tns), len(tax_labels))
for taxon, taxon_label in zip(tns, tax_labels):
self.assertEqual(taxon.label, taxon_label)
def test_basic_new_tree_list(self):
ds = dendropy.DataSet()
item_labels = ["a", "b", "c", "d", "e"]
item_list = []
for item_idx, item_label in enumerate(item_labels):
item = ds.new_tree_list(label=item_label)
item_list.append(item)
self.assertEqual(len(ds.tree_lists), len(item_labels))
self.assertEqual(len(ds.tree_lists), len(item_list))
for t1, t2, label in zip(ds.tree_lists, item_list, item_labels):
self.assertTrue(isinstance(t1, dendropy.TreeList))
self.assertIs(t1, t2)
self.assertEqual(t1.label, label)
def test_basic_new_char_matrix(self):
ds = dendropy.DataSet()
item_labels = ["a", "b", "c", "d", "e", "f"]
cm_type = [
"dna",
"protein",
"standard",
dendropy.DnaCharacterMatrix,
dendropy.ProteinCharacterMatrix,
dendropy.StandardCharacterMatrix,
]
expected_cm_types = [
dendropy.DnaCharacterMatrix,
dendropy.ProteinCharacterMatrix,
dendropy.StandardCharacterMatrix,
dendropy.DnaCharacterMatrix,
dendropy.ProteinCharacterMatrix,
dendropy.StandardCharacterMatrix,
]
item_list = []
for item_label, cm_type in zip(item_labels, cm_type):
item = ds.new_char_matrix(label=item_label,
char_matrix_type=cm_type)
item_list.append(item)
self.assertEqual(len(ds.char_matrices), len(item_labels))
self.assertEqual(len(ds.char_matrices), len(item_list))
for t1, t2, label, expected_cm_types in zip(ds.char_matrices, item_list, item_labels, expected_cm_types):
self.assertTrue(isinstance(t1, expected_cm_types))
self.assertIs(t1, t2)
self.assertEqual(t1.label, label)
class DataSetAttachedTaxonNamespaceModeTestCase(dendropytest.ExtendedTestCase):
def test_attached_taxon_namespace_default(self):
ds = dendropy.DataSet()
tns = dendropy.TaxonNamespace()
ds.attach_taxon_namespace(tns)
self.assertTrue(isinstance(tns, dendropy.TaxonNamespace))
self.assertEqual(len(ds.taxon_namespaces), 1)
self.assertIn(tns, ds.taxon_namespaces)
self.assertIs(ds.taxon_namespaces[0], tns)
self.assertIs(ds.attached_taxon_namespace, tns)
tns2 = ds.detach_taxon_namespace()
self.assertIs(ds.attached_taxon_namespace, None)
self.assertIs(tns2, tns)
def test_attached_taxon_namespace_new_tree_list(self):
ds = dendropy.DataSet()
tns = dendropy.TaxonNamespace()
ds.attach_taxon_namespace(tns)
tree_list = ds.new_tree_list(label="q")
self.assertEqual(tree_list.label, "q")
self.assertIn(tree_list, ds.tree_lists)
self.assertIs(tree_list.taxon_namespace, ds.attached_taxon_namespace)
self.assertEqual(len(ds.taxon_namespaces), 1)
def test_attached_taxon_namespace_new_char_matrix(self):
ds = dendropy.DataSet()
tns = dendropy.TaxonNamespace()
ds.attach_taxon_namespace(tns)
char_matrix = ds.new_char_matrix(label="q", char_matrix_type="dna")
self.assertEqual(char_matrix.label, "q")
self.assertIn(char_matrix, ds.char_matrices)
self.assertIs(char_matrix.taxon_namespace, ds.attached_taxon_namespace)
self.assertEqual(len(ds.taxon_namespaces), 1)
if __name__ == "__main__":
unittest.main()
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