def test1000T(self): sd = SequenceDataset() fp = data_source_path('1000T.fasta') sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA') fp = data_source_path('1000T.tree') tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU")) self.assertEqual(len(tree_list), 1)
def testCentroidEdge(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_centroid(t)
def testDNAFasta(self): sd = SequenceDataset() fp = data_source_path('anolis.fasta') sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')