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_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)