def main():
# register command line arguments
model = CTDModel(
name='NameOfThePyTOPPTool', # required
version='1.0', # required
description=
'This is an example tool how to write pyTOPP tools compatible with the OpenMS workflow ecosystem.',
manual='RTF',
docurl='http://dummy.url/docurl.html',
category='Example',
executableName='exampletool',
executablePath='/path/to/exec/exampletool-1.0/exampletool')
# Register in / out etc. with CTDModel
model.add(
'input',
required=True,
type='input-file',
is_list=False,
file_formats=['mzML'], # filename restrictions
description='Input file')
model.add(
'output',
required=True,
type='output-file',
is_list=False,
file_formats=['mzML'], # filename restrictions
description='Output file')
defaults = pms.PeakPickerHiRes().getDefaults()
# expose algorithm parameters in command line options
addParamToCTDopts(defaults, model)
# parse command line
# if -write_ini is provided, store model in CTD file, exit with error code 0
# if -ini is provided, load CTD file into defaults Param object and return new model with paraneters set as defaults
arg_dict, openms_params = parseCTDCommandLine(sys.argv, model, defaults)
# data processing
fh = pms.MzMLFile()
fh.setLogType(pms.LogType.CMD)
input_map = pms.MSExperiment()
fh.load(arg_dict["input"], input_map)
pp = pms.PeakPickerHiRes()
pp.setParameters(openms_params)
out_map = pms.MSExperiment()
pp.pickExperiment(input_map, out_map)
out_map = addDataProcessing(
out_map, openms_params,
pms.DataProcessing.ProcessingAction.PEAK_PICKING)
fh = pms.FileHandler()
fh.storeExperiment(arg_dict["output"], out_map)
def __init__(self, **modified_config):
self.pp = pyopenms.PeakPickerHiRes()
params = self.pp.getParameters()
config = self.standardConfig
config.update(modified_config)
params.update(config)
self.pp.setParameters(params)
def fft_pick(spec, fft_low_cutoff, fft_high_cutoff):
# filter spec
filtered_spec = fft_filter_spec(spec, fft_low_cutoff, fft_high_cutoff)
# apply pyopenms peakpicker on filtered spec
picker = pyopenms.PeakPickerHiRes()
newspec_out = pyopenms.MSSpectrum()
picker.pick(filtered_spec, newspec_out)
return newspec_out
def main(options):
# generate fragmentationtype lookup
lookup = {}
methods = pyopenms.ActivationMethod()
for attr in dir(methods):
value = getattr(methods,attr)
if isinstance(value,int):
lookup[value] = attr
print "loading MS Experiment "
exp = pyopenms.MSExperiment()
fh = pyopenms.FileHandler()
fh.loadExperiment(options.infile,exp)
print "checking spectra types:"
fragmentationTypes = {}
for s in exp:
typ = getSpectrumType(s,lookup)
cont = continousSpectrumCheck(s)
fragmentationTypes[typ] = fragmentationTypes.get(typ, [] ) + [cont]
isContinousSpectrum = {}
for typ in fragmentationTypes:
check = percentile75(fragmentationTypes[typ])
isContinousSpectrum[typ] = check
if check == True:
print "\t" + typ + " has continous spectra data"
else:
print "\t" + typ + " has centroided spectra data"
print "picking spectra"
expNew = pyopenms.MSExperiment()
picker = pyopenms.PeakPickerHiRes()
for s in exp:
typ = getSpectrumType(s,lookup)
if isContinousSpectrum[typ] == True:
newSpec = pyopenms.MSSpectrum()
picker.pick(s,newSpec)
expNew.addSpectrum(newSpec)
else:
expNew.addSpectrum(s)
print "saving file to ",options.outfile
mzFile = pyopenms.MzMLFile()
fileoptions = mzFile.getOptions()
fileoptions.setCompression(True)
mzFile.setOptions(fileoptions)
mzFile.store(options.outfile,expNew)
print "finished"
def run_peak_picker(input_map, params, out_path):
spec0 = input_map[0]
if pms.PeakTypeEstimator().estimateType(spec0) == \
pms. SpectrumSettings.SpectrumType.PEAKS:
logging.warn("input peak map does not look like profile data")
pp = pms.PeakPickerHiRes()
pp.setParameters(params)
out_map = pms.MSExperiment()
pp.pickExperiment(input_map, out_map)
out_map = addDataProcessing(out_map, params)
fh = pms.FileHandler()
fh.storeExperiment(out_path, out_map)
def run_peak_picker(self):
self._log('Starting peak picking.')
if self.peak_picking_iterative:
self.pp = oms.PeakPickerIterative()
else:
self.pp = oms.PeakPickerHiRes()
self.centroid_out_map = oms.MSExperiment()
self.pp.pickExperiment(self.profile_map, self.centroid_out_map)
self.centroid_out_map.updateRanges()
def run_peak_picker(input_map, params, out_path):
spec0 = input_map[0]
if pms.PeakTypeEstimator().estimateType(spec0) == \
pms. SpectrumSettings.SpectrumType.PEAKS:
logging.warn("input peak map does not look like profile data")
if any(not s.isSorted() for s in input_map):
raise Exception("Not all spectra are sorted according to m/z")
pp = pms.PeakPickerHiRes()
pp.setParameters(params)
out_map = pms.MSExperiment()
pp.pickExperiment(input_map, out_map)
out_map = addDataProcessing(
out_map, params, pms.DataProcessing.ProcessingAction.PEAK_PICKING)
fh = pms.FileHandler()
fh.storeExperiment(out_path, out_map)
def __init__(self, **kwargs):
super(PPEntity, self).__init__(
oms.PeakPickerHiRes(),
**kwargs,
)
def main():
parser = argparse.ArgumentParser(description="PeakPickerHiRes")
parser.add_argument(
"-in",
action="store",
type=str,
dest="in_",
metavar="input_file",
)
parser.add_argument(
"-out",
action="store",
type=str,
metavar="output_file",
)
parser.add_argument(
"-ini",
action="store",
type=str,
metavar="ini_file",
)
parser.add_argument(
"-dict_ini",
action="store",
type=str,
metavar="python_dict_ini_file",
)
parser.add_argument(
"-write_ini",
action="store",
type=str,
metavar="ini_file",
)
parser.add_argument(
"-write_dict_ini",
action="store",
type=str,
metavar="python_dict_ini_file",
)
args = parser.parse_args()
run_mode = args.in_ is not None and args.out is not None\
and (args.ini is not None or args.dict_ini is not None)
write_mode = args.write_ini is not None or args.write_dict_ini is not None
ok = run_mode or write_mode
if not ok:
parser.error("either specify -in, -out and -(dict)ini for running "
"the peakpicker\nor -write(dict)ini for creating std "
"ini file")
defaults = pms.PeakPickerHiRes().getDefaults()
if args.write_dict_ini or args.write_ini:
if args.write_dict_ini:
with open(args.write_dict_ini, "w") as fp:
pprint.pprint(defaults.asDict(), stream=fp)
if args.write_ini:
defaults.store(args.write_ini)
else:
if args.ini:
param = pms.Param()
param.load(args.ini)
defaults.update(param, False, False)
elif args.dict_ini:
with open(args.dict_ini, "r") as fp:
try:
dd = eval(fp.read())
except:
raise Exception("could not parse %s" % args.dict_ini)
defaults.updateFrom(dd)
fh = pms.MzXMLFile()
fh.setLogType(pms.LogType.CMD)
input_map = pms.MSExperiment()
fh.load(args.in_, input_map)
run_peak_picker(input_map, defaults, args.out)
def main():
parser = argparse.ArgumentParser(description="PeakPickerHiRes")
parser.add_argument(
"-in",
action="store",
type=str,
dest="in_",
metavar="input_file",
)
parser.add_argument(
"-out",
action="store",
type=str,
metavar="output_file",
)
parser.add_argument(
"-ini",
action="store",
type=str,
metavar="ini_file",
)
parser.add_argument(
"-dict_ini",
action="store",
type=str,
metavar="python_dict_ini_file",
)
parser.add_argument(
"-write_ini",
action="store",
type=str,
metavar="ini_file",
)
parser.add_argument(
"-write_dict_ini",
action="store",
type=str,
metavar="python_dict_ini_file",
)
args = parser.parse_args()
run_mode = args.in_ is not None and args.out is not None\
and (args.ini is not None or args.dict_ini is not None)
write_mode = args.write_ini is not None or args.write_dict_ini is not None
ok = run_mode or write_mode
if not ok:
parser.error("either specify -in, -out and -(dict)ini for running "
"the peakpicker\nor -write(dict)ini for creating std "
"ini file")
defaults = pms.PeakPickerHiRes().getDefaults()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
fh = pms.MzMLFile()
fh.setLogType(pms.LogType.CMD)
input_map = pms.MSExperiment()
fh.load(args.in_, input_map)
run_peak_picker(input_map, defaults, args.out)
def find_features(self, pp_type: str, peak_radius: int,
window_radius: float, pp_mode: str, ff_type: str,
dir: str, filter: str,
debug: bool) -> List[List[ms.FeatureMap]]:
"""Runs optional peak picking and then an existing feature finder on each IM bin.
Keyword arguments:
pp_type: the peak picker to use ('none', 'pphr', or 'custom')
peak_radius: for the custom peak picker, the minimum peak radius of a peak set
window_radius: for the custom peak picker, the maximum m/z window radius to consider
pp_mode: for the custom peak picker, the mode to use ('ltr' or 'int')
ff_type: the existing feature finder to use ('centroided' or 'multiplex')
dir: the directory to write the intermediate output files to
filter: the noise filter to use ('none', 'gauss', or 'sgolay')
debug: determines if intermediate output files should be written
Returns: a list of two lists (for the passes), each containing the features for all of
their bins.
"""
features = [[], []]
total_features = [ms.FeatureMap(),
ms.FeatureMap()] # Only used for debug output
if filter == 'gauss':
filter_g = ms.GaussFilter()
params_g = filter_g.getDefaults()
params_g.setValue(b'ppm_tolerance', 20.0)
params_g.setValue(b'use_ppm_tolerance', b'true')
filter_g.setParameters(params_g)
if filter == 'sgolay':
filter_s = ms.SavitzkyGolayFilter()
params_s = filter_s.getDefaults()
params_s.setValue(b'frame_length', 7)
params_s.setValue(b'polynomial_order', 3)
filter_s.setParameters(params_s)
pick_hr = ms.PeakPickerHiRes()
pick_im = ppim.PeakPickerIonMobility()
nb = [self.num_bins, 0 if self.num_bins == 1 else self.num_bins + 1
] # Size of each pass
for j in range(2): # Pass index
for i in range(nb[j]): # Bin index
exp, new_exp = ms.MSExperiment(), ms.MSExperiment()
ms.MzMLFile().load(
dir + '/b-' + str(j) + '-' + str(i) + '.mzML', exp)
# Optional noise filtering
if filter == 'gauss':
filter_g.filterExperiment(exp)
elif filter == 'sgolay':
filter_s.filterExperiment(exp)
if filter != 'none' and debug:
ms.MzMLFile().store(
dir + '/pass' + str(j) + '-bin' + str(i) +
'-filtered.mzML', exp)
# Optional peak picking
if pp_type == 'pphr':
pick_hr.pickExperiment(exp, new_exp)
elif pp_type == 'custom':
new_exp = pick_im.pick_experiment(exp,
peak_radius,
window_radius,
pp_mode,
self.MIN_INTENSITY,
strict=True)
else:
new_exp = exp
if pp_type != 'none' and debug:
ms.MzMLFile().store(
dir + '/pass' + str(j) + '-bin' + str(i) +
'-picked.mzML', new_exp)
# Feature finding
temp_features = ms.FeatureMap()
if util.has_peaks(new_exp):
temp_features = self.run_ff(new_exp, ff_type)
temp_features = self.match_features_internal(temp_features)
temp_features.setUniqueIds()
if debug:
ms.FeatureXMLFile().store(
dir + '/pass' + str(j) + '-bin' + str(i) +
'.featureXML', temp_features)
features[j].append(temp_features)
total_features[j] += temp_features
if debug:
for j in range(2):
total_features[j].setUniqueIds()
ms.FeatureXMLFile().store(
dir + '/pass' + str(j) + '.featureXML', total_features[j])
return features[0], features[1]
print("A spectrum is not sorted")
quit()
# Parameters, default [type, constraints, default value]
signal_to_noise = 0.0 # float, 0+, 0
ms_levels = [ 1 ]
win_len = 100.0 # float, 1+, 200
bin_count = 20 # int, 3+, 30
min_required_elements = 5 # int, 1+, 10
# Parameters, advanced (not currently iterating through these)
spacing_difference_gap = 4.0 # float, 0+, 4
spacing_difference = 1.5 # float, 0+, 1.5
missing = 1 # int, 0+, 1
params = ms.PeakPickerHiRes().getParameters()
params.__setitem__(b'ms_levels', ms_levels)
params.__setitem__(b'spacing_difference_gap', spacing_difference_gap)
params.__setitem__(b'spacing_difference', spacing_difference)
params.__setitem__(b'missing', missing)
# Iterate through the params, and for each set, run PeakPickerHiRes and
# FeatureFinderCentroided, and save the param sets for those that find at least the
# target number of features
file = open(args.output + "/suitable_params.txt", "w+")
for stn in np.arange(signal_to_noise, 1.5, 0.25):
params.__setitem__(b'signal_to_noise', stn)