def setUp(self):
self.read_loader = yield_reads(self.read_file)
self.client = GuppyBasecallerClient(config_name=self.config_fast,
port=self.port,
trace=True,
state=True)
self.client.connect()
def basecall(files: List[str], config: str = 'dna_r9.4.1_450bps_fast') -> Tuple[ReadData, CalledReadData]:
with GuppyBasecallerClient(config_name=config, trace=True) as client:
for file in files:
for read in yield_reads(file):
called = client.basecall(read)[1]
yield read, called
class ClientTest(TestCase):
port = 5555
read_file = "tests/reads/testdata/single/read1.fast5"
config_hac = os.environ.get("CONFIG_HAC", "dna_r9.4.1_450bps_hac")
config_fast = os.environ.get("CONFIG_FAST", "dna_r9.4.1_450bps_fast")
def setUp(self):
self.read_loader = yield_reads(self.read_file)
self.client = GuppyBasecallerClient(config_name=self.config_fast,
port=self.port,
trace=True,
state=True)
self.client.connect()
def tearDown(self):
self.client.disconnect()
def test_get_configs(self):
""" test loaded configs """
self.assertTrue(self.config_fast in
[Config(c).name for c in self.client.get_configs()])
def test_without_read(self):
""" test the client api without sending a read """
self.client.get_statistics()
self.client.get_configs()
def test_read_without_state(self):
""" test a read without state """
self.client.pass_read(next(self.read_loader))
time.sleep(1)
self.client._get_called_read()
@skip("skipping")
def test_read_with_state(self):
""" test a read with state """
self.client.pass_read(next(self.read_loader))
time.sleep(1)
res, called = self.client._get_called_read()
self.assertTrue(called.state is not None)
self.assertTrue(called.trace is not None)
self.assertTrue(called.move is not None)
def test_invalid_config(self):
""" try and load in invalid config """
bad_client = GuppyBasecallerClient(config_name="not_a_config",
port=self.port)
with self.assertRaises(ConnectionError):
bad_client.connect()
def test_invalid_config(self):
""" try and load in invalid config """
bad_client = GuppyBasecallerClient(config_name="not_a_config",
port=self.port)
with self.assertRaises(ConnectionError):
bad_client.connect()