import unittest import datetime import logging import os from pasta.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled from pasta import get_logger from pasta.tree import PhylogeneticTree from pasta.alignment import SequenceDataset from pasta.treeholder import read_and_encode_splits from pasta.pastaalignerjob import bisect_tree TOL = 0.000001 _LOG = get_logger(__name__) config = get_testing_configuration() class DecompTest(unittest.TestCase): def testLongestEdge(self): sd = SequenceDataset() fp = data_source_path('100T.fasta') sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA') fp = data_source_path('100T.tree') tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU")) self.assertEqual(len(tree_list), 1) t = PhylogeneticTree(tree_list[0]) self._do_test_longest(t) def testCentroidEdge(self): sd = SequenceDataset()