class FlowDataTestCase(unittest.TestCase):
def setUp(self):
self.maxDiff = None
self.flow_data = FlowData('examples/fcs_files/3FITC_4PE_004.fcs')
self.flow_data_spill = FlowData('examples/fcs_files/100715.fcs')
def test_get_points(self):
self.assertEqual(
len(self.flow_data.events) / self.flow_data.channel_count,
int(self.flow_data.text['tot']))
def test_get_text(self):
self.assertEqual(self.flow_data.text['cyt'], 'FACScan')
@staticmethod
def test_load_fcs_from_memory():
with open('examples/fcs_files/3FITC_4PE_004.fcs', 'rb') as f:
mem_file = io.BytesIO(f.read())
FlowData(mem_file)
def test_load_non_file_input(self):
non_file = object()
self.assertRaises(TypeError, FlowData, non_file)
def test_write_fcs(self):
file_name = 'flowio/tests/flowio_test_write_fcs.fcs'
self.flow_data_spill.write_fcs(file_name)
fcs_export = FlowData(file_name)
self.assertIsInstance(fcs_export, FlowData)
os.unlink(file_name)
def test_write_fcs_preserves_channels(self):
orig_fd = FlowData('examples/fcs_files/100715.fcs')
expected = orig_fd.channels
with tempfile.NamedTemporaryFile() as tmpfile:
orig_fd.write_fcs(tmpfile.name)
out_data = FlowData(tmpfile.name)
actually = out_data.channels
self.assertDictEqual(expected, actually)
def test_issue_03(self):
"""
Tests Attune FCS files for error in FlowData method parse_float_data:
flowio/flowdata.py in __parse_float_data(self, offset, start, stop, data_type, order)
256
257 tmp = unpack('%s%d%s' % (order, num_items, data_type),
--> 258 self.__read_bytes(offset, start, stop))
259 return tmp
260
error: unpack requires a buffer of 277676 bytes
"""
flow_data = FlowData('examples/fcs_files/G11.fcs')
self.assertIsInstance(flow_data, FlowData)
def test_write_fcs_preserves_channels(self):
orig_fd = FlowData('examples/fcs_files/100715.fcs')
expected = orig_fd.channels
with tempfile.NamedTemporaryFile() as tmpfile:
orig_fd.write_fcs(tmpfile.name)
out_data = FlowData(tmpfile.name)
actually = out_data.channels
self.assertDictEqual(expected, actually)
def test_load_temp_file(self):
with tempfile.TemporaryFile() as tmp_file:
with open('examples/fcs_files/3FITC_4PE_004.fcs', 'r+b') as f:
shutil.copyfileobj(f, tmp_file)
tmp_file.seek(0)
out_data = FlowData(tmp_file)
self.assertIsInstance(out_data, FlowData)
def test_write_fcs(self):
file_name = 'flowio/tests/flowio_test_write_fcs.fcs'
self.flow_data_spill.write_fcs(file_name)
fcs_export = FlowData(file_name)
self.assertIsInstance(fcs_export, FlowData)
os.unlink(file_name)
def test_parse_var_int_data(self):
event_values = [
49135, 61373, 48575, 49135, 61373, 48575, 7523, 598, 49135, 61373,
48575, 49135, 61373, 48575, 28182, 61200, 48575, 49135, 32445,
30797, 19057, 49135, 61373, 48575, 5969, 142482809, 61266, 48575,
49135, 20925, 61265, 48575, 27961, 25200, 61287, 48575, 9795,
49135, 29117, 49135, 61373, 48575, 61228, 48575, 22, 21760, 49135,
20413, 49135, 23997, 19807, 3220139858
]
fcs_file = "examples/fcs_files/variable_int_example.fcs"
sample = FlowData(fcs_file)
self.assertListEqual(event_values, sample.events)
def test_create_fcs(self):
event_data = self.flow_data.events
channel_names = self.flow_data.channels
pnn_labels = [v['PnN'] for k, v in channel_names.items()]
export_file_path = "examples/fcs_files/test_fcs_export.fcs"
fh = open(export_file_path, 'wb')
create_fcs(event_data, channel_names=pnn_labels, file_handle=fh)
fh.close()
exported_flow_data = FlowData(export_file_path)
os.unlink(export_file_path)
self.assertIsInstance(exported_flow_data, FlowData)
def test_issue_03(self):
"""
Tests Attune FCS files for error in FlowData method parse_float_data:
flowio/flowdata.py in __parse_float_data(self, offset, start, stop, data_type, order)
256
257 tmp = unpack('%s%d%s' % (order, num_items, data_type),
--> 258 self.__read_bytes(offset, start, stop))
259 return tmp
260
error: unpack requires a buffer of 277676 bytes
"""
flow_data = FlowData('examples/fcs_files/G11.fcs')
self.assertIsInstance(flow_data, FlowData)
def setUp(self):
self.flow_data = FlowData('examples/fcs_files/coulter.lmd')
def setUp(self):
self.flowdata = FlowData('sample_data/coulter.lmd')
def setUp(self):
self.maxDiff = None
self.flow_data = FlowData('examples/fcs_files/3FITC_4PE_004.fcs')
self.flow_data_spill = FlowData('examples/fcs_files/100715.fcs')
class FlowDataTestCase(unittest.TestCase):
def setUp(self):
self.maxDiff = None
self.flow_data = FlowData('examples/fcs_files/3FITC_4PE_004.fcs')
self.flow_data_spill = FlowData('examples/fcs_files/100715.fcs')
def test_string_representation(self):
self.assertEqual(str(self.flow_data), "FlowData(3FITC_4PE_004.fcs)")
def test_get_points(self):
self.assertEqual(
len(self.flow_data.events) / self.flow_data.channel_count,
int(self.flow_data.text['tot']))
def test_get_text(self):
self.assertEqual(self.flow_data.text['cyt'], 'FACScan')
@staticmethod
def test_load_fcs_from_memory():
with open('examples/fcs_files/3FITC_4PE_004.fcs', 'rb') as f:
mem_file = io.BytesIO(f.read())
FlowData(mem_file)
def test_load_temp_file(self):
with tempfile.TemporaryFile() as tmp_file:
with open('examples/fcs_files/3FITC_4PE_004.fcs', 'r+b') as f:
shutil.copyfileobj(f, tmp_file)
tmp_file.seek(0)
out_data = FlowData(tmp_file)
self.assertIsInstance(out_data, FlowData)
def test_load_non_file_input(self):
non_file = object()
self.assertRaises(AttributeError, FlowData, non_file)
def test_write_fcs(self):
file_name = 'flowio/tests/flowio_test_write_fcs.fcs'
self.flow_data_spill.write_fcs(file_name)
fcs_export = FlowData(file_name)
self.assertIsInstance(fcs_export, FlowData)
os.unlink(file_name)
def test_parse_var_int_data(self):
event_values = [
49135, 61373, 48575, 49135, 61373, 48575, 7523, 598, 49135, 61373,
48575, 49135, 61373, 48575, 28182, 61200, 48575, 49135, 32445,
30797, 19057, 49135, 61373, 48575, 5969, 142482809, 61266, 48575,
49135, 20925, 61265, 48575, 27961, 25200, 61287, 48575, 9795,
49135, 29117, 49135, 61373, 48575, 61228, 48575, 22, 21760, 49135,
20413, 49135, 23997, 19807, 3220139858
]
fcs_file = "examples/fcs_files/variable_int_example.fcs"
sample = FlowData(fcs_file)
self.assertListEqual(event_values, sample.events)
def test_write_fcs_preserves_channels(self):
orig_fd = FlowData('examples/fcs_files/100715.fcs')
expected = orig_fd.channels
with tempfile.NamedTemporaryFile() as tmpfile:
orig_fd.write_fcs(tmpfile.name)
out_data = FlowData(tmpfile.name)
actually = out_data.channels
self.assertDictEqual(expected, actually)
def test_issue_03(self):
"""
Tests Attune FCS files for error in FlowData method parse_float_data:
flowio/flowdata.py in __parse_float_data(self, offset, start, stop, data_type, order)
256
257 tmp = unpack('%s%d%s' % (order, num_items, data_type),
--> 258 self.__read_bytes(offset, start, stop))
259 return tmp
260
error: unpack requires a buffer of 277676 bytes
"""
flow_data = FlowData('examples/fcs_files/G11.fcs')
self.assertIsInstance(flow_data, FlowData)
def test_load_fcs_from_memory():
with open('examples/fcs_files/3FITC_4PE_004.fcs', 'rb') as f:
mem_file = io.BytesIO(f.read())
FlowData(mem_file)
def setUp(self):
self.flowdata = FlowData('sample_data/3FITC_4PE_004.fcs')
def test_load_fcs():
for unused in range(100):
FlowData('sample_data/3FITC_4PE_004.fcs')
def setUp(self):
self.flow_data = FlowData('examples/fcs_files/100715.fcs')