def test_TopN_controller_with_simulated_chems(self, fragscan_dataset):
logger.info(
'Testing Top-N controller with simulated chemicals -- no noise')
assert len(fragscan_dataset) == N_CHEMS
isolation_width = 1
N = 10
rt_tol = 15
mz_tol = 10
ionisation_mode = POSITIVE
# create a simulated mass spec without noise and Top-N controller
mass_spec = IndependentMassSpectrometer(ionisation_mode,
fragscan_dataset)
controller = TopNController(ionisation_mode, N, isolation_width,
mz_tol, rt_tol, MIN_MS1_INTENSITY)
min_bound, max_bound = get_rt_bounds(fragscan_dataset, CENTRE_RANGE)
# create an environment to run both the mass spec and controller
env = Environment(mass_spec,
controller,
min_bound,
max_bound,
progress_bar=True)
run_environment(env)
# check that there is at least one non-empty MS2 scan
check_non_empty_MS2(controller)
filename = 'topN_controller_simulated_chems_no_noise.mzML'
check_mzML(env, OUT_DIR, filename)
def test_intensity_nonoverlap_controller_with_simulated_chems(
self, fragscan_dataset):
logger.info(
'Testing intensity non-overlap controller with simulated chemicals'
)
assert len(fragscan_dataset) == N_CHEMS
isolation_width = 1 # the isolation window in Dalton around a selected precursor ion
N = 10
rt_tol = 15
mz_tol = 10
min_roi_intensity = 50
min_roi_length = 0
ionisation_mode = POSITIVE
min_bound, max_bound = get_rt_bounds(fragscan_dataset, CENTRE_RANGE)
rt_box_size, mz_box_size = 1, 0.3
# create a simulated mass spec with noise and ROI controller
mass_spec = IndependentMassSpectrometer(ionisation_mode,
fragscan_dataset)
grid = GridEstimator(
AllOverlapGrid(min_bound, max_bound, rt_box_size, 0, 3000,
mz_box_size), IdentityDrift())
controller = IntensityNonOverlapController(
ionisation_mode,
isolation_width,
mz_tol,
MIN_MS1_INTENSITY,
min_roi_intensity,
min_roi_length,
N,
grid,
rt_tol=rt_tol,
min_roi_length_for_fragmentation=0)
# create an environment to run both the mass spec and controller
env = Environment(mass_spec,
controller,
min_bound,
max_bound,
progress_bar=True)
run_environment(env)
assert len(controller.scans[2]) > 0
# check that there is at least one non-empty MS2 scan
check_non_empty_MS2(controller)
# write simulated output to mzML file
filename = 'intensity_non_overlap_controller_simulated_chems.mzML'
check_mzML(env, OUT_DIR, filename)
def test_ms1_controller_with_simulated_chems(self, fragscan_dataset):
logger.info('Testing MS1 controller with simulated chemicals')
min_bound, max_bound = get_rt_bounds(fragscan_dataset, CENTRE_RANGE)
logger.info('RT bounds %s %s' % (min_bound, max_bound))
assert len(fragscan_dataset) == N_CHEMS
# create a simulated mass spec and MS1 controller
mass_spec = IndependentMassSpectrometer(POSITIVE, fragscan_dataset)
controller = SimpleMs1Controller()
# create an environment to run both the mass spec and controller
env = Environment(mass_spec, controller, min_bound, max_bound, progress_bar=True)
run_environment(env)
# write simulated output to mzML file
filename = 'ms1_controller_simulated_chems.mzML'
check_mzML(env, OUT_DIR, filename)
def test_smart_roi_controller_with_simulated_chems(self, fragscan_dataset):
logger.info('Testing ROI controller with simulated chemicals')
assert len(fragscan_dataset) == N_CHEMS
isolation_width = 1 # the isolation window in Dalton around a selected precursor ion
N = 10
rt_tol = 15
mz_tol = 10
min_roi_intensity = 50
min_roi_length = 0
ionisation_mode = POSITIVE
# create a simulated mass spec with noise and ROI controller
mass_spec = IndependentMassSpectrometer(ionisation_mode,
fragscan_dataset)
controller = TopN_SmartRoiController(
ionisation_mode,
isolation_width,
mz_tol,
MIN_MS1_INTENSITY,
min_roi_intensity,
min_roi_length,
N,
rt_tol,
min_roi_length_for_fragmentation=0)
# create an environment to run both the mass spec and controller
min_bound, max_bound = get_rt_bounds(fragscan_dataset, CENTRE_RANGE)
env = Environment(mass_spec,
controller,
min_bound,
max_bound,
progress_bar=True)
run_environment(env)
assert len(controller.scans[2]) > 0
# check that there is at least one non-empty MS2 scan
check_non_empty_MS2(controller)
# write simulated output to mzML file
filename = 'smart_roi_controller_simulated_chems.mzML'
check_mzML(env, OUT_DIR, filename)
def test_AIF_controller_with_simulated_chems(self, fragscan_dataset):
logger.info('Testing Top-N controller with simulated chemicals')
# create some chemical object
assert len(fragscan_dataset) == N_CHEMS
# isolation_width = 1
# N = 10
# rt_tol = 15
# mz_tol = 10
ionisation_mode = POSITIVE
min_mz = 100
max_mz = 500
# shorten the rt range for quicker tests
# min_rt = 0
# max_rt = 400
scan_time_dict = {1: 0.12, 2: 0.06}
# create a simulated mass spec without noise and Top-N controller
logger.info('Without noise')
mass_spec = IndependentMassSpectrometer(ionisation_mode, fragscan_dataset,
scan_duration=scan_time_dict)
params = AdvancedParams(default_ms1_scan_window=[min_mz, max_mz])
ms1_source_cid_energy = 30
controller = AIF(ms1_source_cid_energy, params=params)
# create an environment to run both the mass spec and controller
min_bound, max_bound = get_rt_bounds(fragscan_dataset, CENTRE_RANGE)
env = Environment(mass_spec, controller, min_bound, max_bound, progress_bar=True)
# set the log level to WARNING so we don't see too many messages when
# environment is running
set_log_level_warning()
# run the simulation
env.run()
# set the log level back to DEBUG
set_log_level_debug()
# write simulated output to mzML file
filename = 'AIF_simulated_chems_no_noise.mzML'
check_mzML(env, OUT_DIR, filename)
# create a simulated mass spec with noise and Top-N controller
logger.info('With noise')
mz_noise = GaussianPeakNoiseLevelSpecific({2: 0.01})
intensity_noise = GaussianPeakNoiseLevelSpecific({2: 1000.})
mass_spec = IndependentMassSpectrometer(ionisation_mode, fragscan_dataset,
mz_noise=mz_noise,
intensity_noise=intensity_noise,
scan_duration=scan_time_dict)
params = AdvancedParams(default_ms1_scan_window=[min_mz, max_mz])
ms1_source_cid_energy = 30
controller = AIF(ms1_source_cid_energy, params=params)
# create an environment to run both the mass spec and controller
min_bound, max_bound = get_rt_bounds(fragscan_dataset, CENTRE_RANGE)
env = Environment(mass_spec, controller, min_bound, max_bound, progress_bar=True)
# set the log level to WARNING so we don't see too many messages
# when environment is running
set_log_level_warning()
# run the simulation
env.run()
# set the log level back to DEBUG
set_log_level_debug()
# write simulated output to mzML file
filename = 'AIF_simulated_chems_with_noise.mzML'
check_mzML(env, OUT_DIR, filename)