def test_create_temporary_phylip(self, temp_mock):
temp_file = StringIO()
temp_mock.return_value = temp_file
builder = TreeBuilder()
fasta_file = StringIO("""\
>cluster_A
NNAACAAAANN
>cluster_B
CCAACAAAANN
""")
expected_output = """\
2 11
cluster_A NNAACAAAAN N
cluster_B CCAACAAAAN N
"""
builder.load_fasta_sequences(fasta_file)
output_file = builder._create_temporary_phylip(builder.sequences)
self.assertEqual(output_file, temp_file)
output_file.seek(0)
self.assertEqual(output_file.read(), expected_output)
def test_run_fastml(self):
builder = TreeBuilder()
fasta_filename = os.path.join(test_data(), 'animals.mfa')
tree_filename = os.path.join(test_data(),
'animals.terminal_nodes.newick')
output_directory = tempfile.mkdtemp()
# fastml doesn't like comments in fasta files, guesses it is a different
# format and gets confused when a sequence has a '>' in it. I'm therefore
# creating a temporary file without the comments in it.
fasta_file_without_comments = create_fasta_without_comments(
fasta_filename)
fastml_stdout, fastml_stderr = builder._run_fastml(
'fastml', {}, tree_filename, fasta_file_without_comments,
output_directory)
self.assertTrue(
os.path.isfile(os.path.join(output_directory, 'all_nodes.newick')))
self.assertTrue(
os.path.isfile(os.path.join(output_directory, 'all_nodes.mfa')))
shutil.rmtree(output_directory)
os.remove(fasta_file_without_comments)
def test_build_tree(self, temp_mock):
builder = TreeBuilder()
# I could mock _run_raxml but, because I'm using a regex to parse the
# results, I want to know straight away if the output of RAxML changes in a
# way that breaks this.
random_file = tempfile.NamedTemporaryFile('w', delete=False)
random_filename = random_file.name
random_folder = tempfile.mkdtemp()
temp_mock.NamedTemporaryFile.return_value = random_file
temp_mock.mkdtemp.return_value = random_folder
fasta_file = open(os.path.join(test_data(), 'animals.mfa'), 'r')
builder.load_fasta_sequences(fasta_file)
fasta_file.close()
tree = builder.build_tree()
tree_nodes = sorted([node.name for node in tree.get_terminals()])
expected_tree_nodes = ["Carp", "Chicken", "Cow", "Frog", "Human", "Loach",
"Mouse", "Rat", "Seal", "Whale"]
self.assertIsInstance(tree, Bio.Phylo.Newick.Tree)
self.assertEqual(tree_nodes, expected_tree_nodes)
self.assertFalse(os.path.isdir(random_folder))
self.assertFalse(os.path.isfile(random_filename))
def test_build_tree(self, temp_mock):
builder = TreeBuilder()
# I could mock _run_raxml but, because I'm using a regex to parse the
# results, I want to know straight away if the output of RAxML changes in a
# way that breaks this.
random_file = tempfile.NamedTemporaryFile('w', delete=False)
random_filename = random_file.name
random_folder = tempfile.mkdtemp()
temp_mock.NamedTemporaryFile.return_value = random_file
temp_mock.mkdtemp.return_value = random_folder
fasta_file = open(os.path.join(test_data(), 'animals.mfa'), 'r')
builder.load_fasta_sequences(fasta_file)
fasta_file.close()
tree = builder.build_tree()
tree_nodes = sorted([node.name for node in tree.get_terminals()])
expected_tree_nodes = [
"Carp", "Chicken", "Cow", "Frog", "Human", "Loach", "Mouse", "Rat",
"Seal", "Whale"
]
self.assertIsInstance(tree, Bio.Phylo.Newick.Tree)
self.assertEqual(tree_nodes, expected_tree_nodes)
self.assertFalse(os.path.isdir(random_folder))
self.assertFalse(os.path.isfile(random_filename))
def test_create_temporary_phylip(self, temp_mock):
temp_file = StringIO()
temp_mock.return_value = temp_file
builder = TreeBuilder()
fasta_file = StringIO("""\
>cluster_A
NNAACAAAANN
>cluster_B
CCAACAAAANN
""")
expected_output = """\
2 11
cluster_A NNAACAAAAN N
cluster_B CCAACAAAAN N
"""
builder.load_fasta_sequences(fasta_file)
output_file = builder._create_temporary_phylip(builder.sequences)
self.assertEqual(output_file, temp_file)
output_file.seek(0)
self.assertEqual(output_file.read(), expected_output)
def test_write_tree(self):
builder = TreeBuilder()
tree_filename = os.path.join(test_data(), 'animals.terminal_nodes.newick')
tree = Bio.Phylo.read(tree_filename, 'newick')
output = StringIO()
builder._write_tree(tree, output)
with open(tree_filename, 'r') as tree_file:
expected = tree_file.read()
output.seek(0)
self.assertEqual(output.read(), expected)
def test_write_output(self):
builder = TreeBuilder()
builder.sequences = {"seq1": "a sequence object"}
builder.tree = "Tree"
builder.sequences_output_file = StringIO()
builder.tree_output_file = StringIO()
builder._write_tree = MagicMock()
builder._write_sequences = MagicMock()
builder.write_output()
builder._write_tree.assert_called_with("Tree",
builder.tree_output_file)
builder._write_sequences.assert_called_with(
["a sequence object"], builder.sequences_output_file)
def test_write_tree(self):
builder = TreeBuilder()
tree_filename = os.path.join(test_data(),
'animals.terminal_nodes.newick')
tree = Bio.Phylo.read(tree_filename, 'newick')
output = StringIO()
builder._write_tree(tree, output)
with open(tree_filename, 'r') as tree_file:
expected = tree_file.read()
output.seek(0)
self.assertEqual(output.read(), expected)
def test_run_raxml(self):
builder = TreeBuilder()
fasta_file = open(os.path.join(test_data(), 'animals.mfa'), 'r')
builder.load_fasta_sequences(fasta_file)
fasta_file.close()
phylip_file = builder._create_temporary_phylip(builder.sequences)
phylip_file.close()
output_directory = tempfile.mkdtemp()
raxml_stdout, raxml_stderr = builder._run_raxml('raxmlHPC', {}, phylip_file.name, output_directory)
self.assertTrue('Best-scoring ML tree written to' in raxml_stdout)
os.remove(phylip_file.name)
shutil.rmtree(output_directory)
def test_write_sequences(self):
builder = TreeBuilder()
fasta_filename = os.path.join(test_data(), 'animals.mfa')
fasta_file = open(fasta_filename, 'r')
sequences = Bio.SeqIO.parse(fasta_file, 'fasta')
output = StringIO()
builder._write_sequences(sequences, output)
fasta_file.close()
with open(fasta_filename, 'r') as fasta_file:
expected = fasta_file.readlines()
expected = "".join(expected[5:]) # Remove comments from the top
output.seek(0)
self.assertEqual(output.read(), expected)
def test_write_sequences(self):
builder = TreeBuilder()
fasta_filename = os.path.join(test_data(), 'animals.mfa')
fasta_file = open(fasta_filename, 'r')
sequences = Bio.SeqIO.parse(fasta_file, 'fasta')
output = StringIO()
builder._write_sequences(sequences, output)
fasta_file.close()
with open(fasta_filename, 'r') as fasta_file:
expected = fasta_file.readlines()
expected = "".join(expected[5:]) # Remove comments from the top
output.seek(0)
self.assertEqual(output.read(), expected)
def test_write_output(self):
builder = TreeBuilder()
builder.sequences = {"seq1": "a sequence object"}
builder.tree = "Tree"
builder.sequences_output_file = StringIO()
builder.tree_output_file = StringIO()
builder._write_tree = MagicMock()
builder._write_sequences = MagicMock()
builder.write_output()
builder._write_tree.assert_called_with("Tree",
builder.tree_output_file)
builder._write_sequences.assert_called_with(["a sequence object"],
builder.sequences_output_file)
def test_get_raxml_tree_file(self):
builder = TreeBuilder()
fake_stdout = """\
Inference[0] final GAMMA-based Likelihood: -385.279958 tree written to file/tmp/tmpaA9uJN/RAxML_result.raxml_output
Starting final GAMMA-basedthorough Optimization on tree 0 likelihood -385.279958 ....
FinalGAMMA-based Score of best tree -385.279958
Program execution info written to/tmp/tmpaA9uJN/RAxML_info.raxml_output
Best-scoring ML tree written to: /tmp/tmpaA9uJN/RAxML_bestTree.raxml_output
Overall execution time: 0.219131 secs or 0.000061 hours or 0.000003 days
"""
output = builder._get_raxml_tree_file(fake_stdout)
self.assertEqual(output, '/tmp/tmpaA9uJN/RAxML_bestTree.raxml_output')
fake_stdout = """\
Final tree written to: /tmp/tmpaA9uJN/raxml_output
"""
output = builder._get_raxml_tree_file(fake_stdout)
self.assertEqual(output, '/tmp/tmpaA9uJN/raxml_output')
fake_stdout = """\
Oh dear
Something went wrong
I've written something to /tmp/wrong.log
But it is definitly not what you're looking for.
Sorry
"""
output = builder._get_raxml_tree_file(fake_stdout)
self.assertEqual(output, None)
def test_get_raxml_tree_file(self):
builder = TreeBuilder()
fake_stdout = """\
Inference[0] final GAMMA-based Likelihood: -385.279958 tree written to file/tmp/tmpaA9uJN/RAxML_result.raxml_output
Starting final GAMMA-basedthorough Optimization on tree 0 likelihood -385.279958 ....
FinalGAMMA-based Score of best tree -385.279958
Program execution info written to/tmp/tmpaA9uJN/RAxML_info.raxml_output
Best-scoring ML tree written to: /tmp/tmpaA9uJN/RAxML_bestTree.raxml_output
Overall execution time: 0.219131 secs or 0.000061 hours or 0.000003 days
"""
output = builder._get_raxml_tree_file(fake_stdout)
self.assertEqual(output, '/tmp/tmpaA9uJN/RAxML_bestTree.raxml_output')
fake_stdout = """\
Final tree written to: /tmp/tmpaA9uJN/raxml_output
"""
output = builder._get_raxml_tree_file(fake_stdout)
self.assertEqual(output, '/tmp/tmpaA9uJN/raxml_output')
fake_stdout = """\
Oh dear
Something went wrong
I've written something to /tmp/wrong.log
But it is definitly not what you're looking for.
Sorry
"""
output = builder._get_raxml_tree_file(fake_stdout)
self.assertEqual(output, None)
def test_run_fastml(self):
builder = TreeBuilder()
fasta_filename = os.path.join(test_data(), 'animals.mfa')
tree_filename = os.path.join(test_data(), 'animals.terminal_nodes.newick')
output_directory = tempfile.mkdtemp()
# fastml doesn't like comments in fasta files, guesses it is a different
# format and gets confused when a sequence has a '>' in it. I'm therefore
# creating a temporary file without the comments in it.
fasta_file_without_comments = create_fasta_without_comments(fasta_filename)
fastml_stdout, fastml_stderr = builder._run_fastml('fastml', {},
tree_filename,
fasta_file_without_comments,
output_directory)
self.assertTrue(os.path.isfile(os.path.join(output_directory,
'all_nodes.newick')))
self.assertTrue(os.path.isfile(os.path.join(output_directory,
'all_nodes.mfa')))
shutil.rmtree(output_directory)
os.remove(fasta_file_without_comments)
def test_run_raxml(self):
builder = TreeBuilder()
fasta_file = open(os.path.join(test_data(), 'animals.mfa'), 'r')
builder.load_fasta_sequences(fasta_file)
fasta_file.close()
phylip_file = builder._create_temporary_phylip(builder.sequences)
phylip_file.close()
output_directory = tempfile.mkdtemp()
raxml_stdout, raxml_stderr = builder._run_raxml(
'raxmlHPC', {}, phylip_file.name, output_directory)
self.assertTrue('Best-scoring ML tree written to' in raxml_stdout)
os.remove(phylip_file.name)
shutil.rmtree(output_directory)
def test_add_hereditary_nodes(self, temp_mock):
builder = TreeBuilder()
output_directory = tempfile.mkdtemp()
temp_mock.mkdtemp.return_value = output_directory
temp_mock.NamedTemporaryFile.side_effect = \
(tempfile.NamedTemporaryFile(dir=output_directory, delete=False) for i in xrange(10))
fasta_filename = os.path.join(test_data(), 'animals.mfa')
with open(fasta_filename) as fasta_file:
builder.load_fasta_sequences(fasta_file)
tree_filename = os.path.join(test_data(),
'animals.terminal_nodes.newick')
builder.tree = Bio.Phylo.read(tree_filename, 'newick')
builder.add_hereditary_nodes()
self.assertIsInstance(builder.tree, Bio.Phylo.Newick.Tree)
tree_nodes = sorted([node.name for node in builder.tree.find_clades()])
self.assertItemsEqual(tree_nodes, builder.sequences.keys())
self.assertEqual(len(tree_nodes), 19)
self.assertFalse(os.path.isdir(output_directory))
def test_add_hereditary_nodes(self, temp_mock):
builder = TreeBuilder()
output_directory = tempfile.mkdtemp()
temp_mock.mkdtemp.return_value = output_directory
temp_mock.NamedTemporaryFile.side_effect = \
(tempfile.NamedTemporaryFile(dir=output_directory, delete=False) for i in xrange(10))
fasta_filename = os.path.join(test_data(), 'animals.mfa')
with open(fasta_filename) as fasta_file:
builder.load_fasta_sequences(fasta_file)
tree_filename = os.path.join(test_data(), 'animals.terminal_nodes.newick')
builder.tree = Bio.Phylo.read(tree_filename, 'newick')
builder.add_hereditary_nodes()
self.assertIsInstance(builder.tree, Bio.Phylo.Newick.Tree)
tree_nodes = sorted([node.name for node in builder.tree.find_clades()])
self.assertItemsEqual(tree_nodes, builder.sequences.keys())
self.assertEqual(len(tree_nodes), 19)
self.assertFalse(os.path.isdir(output_directory))
