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)