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')