def test_run_metrics_member(self):
"""
Test if the run metrics object is properly wrapped
"""
run_metrics = py_interop_run_metrics.run_metrics()
self.assertEqual(run_metrics.extraction_metric_set().size(), 0)
def test_run_metrics_typedef_wrapping(self):
"""
Test that the metric typedefs in run_metrics are properly wrapped
"""
run_metrics = py_interop_run_metrics.run_metrics()
metric_set_getters = [
method for method in dir(run_metrics)
if method.endswith('metric_set') and not method.startswith('set_')
]
for getter in metric_set_getters:
metric_set = getattr(run_metrics, getter)()
self.assertTrue(hasattr(metric_set, 'size'))
self.assertEqual(metric_set.size(), 0)
def test_plot_qscore_heatmap(self):
"""
Test that plot_flowcell_map is properly wrapped
"""
run = py_interop_run_metrics.run_metrics()
options = py_interop_plot.filter_options(
run.run_info().flowcell().naming_method())
rows = py_interop_plot.count_rows_for_heatmap(run)
cols = py_interop_plot.count_columns_for_heatmap(run)
dataBuffer = numpy.zeros((rows, cols), dtype=numpy.float32)
data = py_interop_plot.heatmap_data()
try:
py_interop_plot.plot_qscore_heatmap(run, options, data,
dataBuffer.ravel())
except py_interop_run.invalid_filter_option:
pass
def test_plot_flowcell_map(self):
"""
Test that plot_flowcell_map is properly wrapped
"""
run = py_interop_run_metrics.run_metrics()
options = py_interop_plot.filter_options(
run.run_info().flowcell().naming_method())
bufferSize = py_interop_plot.calculate_flowcell_buffer_size(
run, options)
dataBuffer = numpy.zeros(bufferSize, dtype=numpy.float32)
idBuffer = numpy.zeros(bufferSize, dtype=numpy.uint32)
data = py_interop_plot.flowcell_data()
try:
py_interop_plot.plot_flowcell_map2(run, py_interop_run.Intensity,
options, data, dataBuffer,
idBuffer)
except py_interop_run.invalid_filter_option:
pass
def test_populate_imaging_table(self):
"""
Test if imaging logic can be properly used
"""
tmp = numpy.asarray([
2, 38, 7, 0, 90, 4, 1, 0, -12, -56, 15, 64, -98, 35, 12, 64, 0, 0,
0, 0, 0, 0, 0, 0, 46, 1, 17, 1, 0, 0, 0, 0, 96, -41, -104, 36, 122,
-86, -46, -120, 7, 0, -66, 4, 1, 0, 96, -43, 14, 64, -63, 49, 13,
64, 0, 0, 0, 0, 0, 0, 0, 0, 56, 1, 17, 1, 0, 0, 0, 0, 112, 125, 77,
38, 122, -86, -46, -120, 7, 0, 66, 8, 1, 0, 74, -68, 6, 64, -118,
-7, 8, 64, 0, 0, 0, 0, 0, 0, 0, 0, 93, 1, 46, 1, 0, 0, 0, 0, -47,
-104, 2, 40, 122, -86, -46, -120
],
dtype=numpy.uint8)
run = py_interop_run_metrics.run_metrics()
py_interop_comm.read_interop_from_buffer(tmp,
run.extraction_metric_set())
self.assertEqual(run.extraction_metric_set().size(), 3)
reads = py_interop_run.read_info_vector()
reads.append(py_interop_run.read_info(1, 1, 26))
reads.append(py_interop_run.read_info(2, 27, 76))
run.run_info(
py_interop_run.info(py_interop_run.flowcell_layout(2, 2, 2, 16),
reads))
run.legacy_channel_update(py_interop_run.HiSeq)
columns = py_interop_table.imaging_column_vector()
py_interop_table.create_imaging_table_columns(run, columns)
row_offsets = py_interop_table.map_id_offset()
py_interop_table.count_table_rows(run, row_offsets)
column_count = py_interop_table.count_table_columns(columns)
data = numpy.zeros((len(row_offsets), column_count),
dtype=numpy.float32)
py_interop_table.populate_imaging_table_data(run, columns, row_offsets,
data.ravel())
self.assertEqual(data[0, 0], 7)