def test_aln_tree_seqs(self): "aln_tree_seqs returns the muscle alignment and tree from iteration2" tree, aln = aln_tree_seqs(path.join(self.temp_dir, 'seq1.txt'), tree_type="neighborjoining", WorkingDir=self.temp_dir, clean_up=True) self.assertEqual(str(tree), '((1:1.125,2:1.125):0.375,3:1.5);') self.assertEqual(len(aln), 6) self.assertEqual(aln[-2], '>3\n') self.assertEqual(aln[-1], 'GCGGCUAUUAGAUCGUA------\n')
def test_aln_tree_seqs_spaces(self): "aln_tree_seqs should work on filename with spaces" try: #create sequence files f = open(path.join(self.temp_dir_spaces, 'muscle_test_seq1.txt'),'w') f.write('\n'.join(self.lines1)) f.close() except OSError: pass tree, aln = aln_tree_seqs(path.join(self.temp_dir_spaces,\ 'muscle_test_seq1.txt'), tree_type="neighborjoining", WorkingDir=getcwd(), clean_up=True) self.assertEqual(str(tree), '((1:1.125,2:1.125):0.375,3:1.5);') self.assertEqual(len(aln), 6) self.assertEqual(aln[-2], '>3\n') self.assertEqual(aln[-1], 'GCGGCUAUUAGAUCGUA------\n') remove(self.temp_dir_spaces+'/muscle_test_seq1.txt')