def test_base_command(self):
"""RdpClassifier should return expected shell command."""
app = RdpClassifier()
exp = ''.join([
'cd "', getcwd(), '/"; java -Xmx1000m -jar "',
self.user_rdp_jar_path, '" -q'])
self.assertEqual(app.BaseCommand, exp)
def test_assign_jvm_parameters(self):
"""RdpCalssifier should pass alternate parameters to Java VM."""
app = RdpClassifier()
app.Parameters['-Xmx'].on('75M')
exp = ''.join([
'cd "', getcwd(), '/"; java -Xmx75M -jar "',
self.user_rdp_jar_path, '" -q'])
self.assertEqual(app.BaseCommand, exp)
def test_change_working_dir(self):
"""RdpClassifier should run program in expected working directory."""
test_dir = '/tmp/RdpTest'
app = RdpClassifier(WorkingDir=test_dir)
exp = ''.join(['cd "', test_dir, '/"; java -Xmx1000m -jar "', self.user_rdp_jar_path, '"'])
self.assertEqual(app.BaseCommand, exp)
rmtree(test_dir)
def test_sample_fasta(self):
"""RdpClassifier should classify its own sample data correctly"""
test_dir = '/tmp/RdpTest'
app = RdpClassifier(WorkingDir=test_dir)
_, output_fp = tempfile.mkstemp(dir=test_dir)
app.Parameters['-o'].on(output_fp)
results = app(StringIO(rdp_sample_fasta))
assignment_toks = results['Assignments'].readline().split('\t')
self.assertEqual(assignment_toks[0], 'X67228')
lineage = [x.strip('"') for x in assignment_toks[2::3]]
self.assertEqual(lineage, [
'Root', 'Bacteria', 'Proteobacteria', 'Alphaproteobacteria',
'Rhizobiales', 'Rhizobiaceae', 'Rhizobium'])
rmtree(test_dir)
def test_sample_fasta(self):
"""RdpClassifier should classify its own sample data correctly"""
test_dir = '/tmp/RdpTest'
app = RdpClassifier(WorkingDir=test_dir)
results = app(rdp_sample_fasta)
results_file = results['StdOut']
id_line = results_file.readline()
self.failUnless(id_line.startswith('>X67228'))
classification_line = results_file.readline().strip()
obs = parse_rdp(classification_line)
exp = ['Root', 'Bacteria', 'Proteobacteria', 'Alphaproteobacteria', 'Rhizobiales', 'Rhizobiaceae', 'Rhizobium']
self.assertEqual(obs, exp)
rmtree(test_dir)
def test_basecommand_property(self):
"""RdpClassifier BaseCommand property should use overridden method."""
app = RdpClassifier()
self.assertEqual(app.BaseCommand, app._get_base_command())
def test_basecommand_property(self):
"""RdpClassifier BaseCommand property should use overridden method."""
app = RdpClassifier()
self.assertEqual(app.BaseCommand, app._get_base_command())
def test_parameters_list(self):
a = RdpClassifier()
parameters = list(a.Parameters.keys())
parameters.sort()
self.assertEqual(parameters, ['-Xmx', '-f', '-o', '-t'])
def test_default_java_vm_parameters(self):
"""RdpClassifier should store default arguments to Java VM."""
a = RdpClassifier()
self.assertContains(a.Parameters, '-Xmx')
self.assertEqual(a.Parameters['-Xmx'].Value, '1000m')
def test_default_positional_parameters(self):
"""RdpClassifier should store default positional arguments."""
a = RdpClassifier()
self.assertContains(a.PositionalParameters, '-training-data')
self.assertEqual(a.PositionalParameters['-training-data'].Value, '')
def test_positional_parameters_list(self):
a = RdpClassifier()
parameters = a.PositionalParameters.keys()
parameters.sort()
self.assertEqual(parameters, ['-training-data'])
def test_jvm_parameters_list(self):
a = RdpClassifier()
parameters = a.JvmParameters.keys()
parameters.sort()
self.assertEqual(parameters, ['-Xmx'])