def algorithm(chromatograms, targeted):
# Create empty files as input and finally as output
empty_swath = pyopenms.MSExperiment()
trafo = pyopenms.TransformationDescription()
output = pyopenms.FeatureMap()
# set up featurefinder and run
featurefinder = pyopenms.MRMFeatureFinderScoring()
# set the correct rt use values
scoring_params = pyopenms.MRMFeatureFinderScoring().getDefaults()
scoring_params.setValue("Scores:use_rt_score", 'false', '')
featurefinder.setParameters(scoring_params)
featurefinder.pickExperiment(chromatograms, output, targeted, trafo,
empty_swath)
# get the pairs
pairs = []
simple_find_best_feature(output, pairs, targeted)
pairs_corrected = pyopenms.MRMRTNormalizer().rm_outliers(pairs, 0.95, 0.6)
pairs_corrected = [list(p) for p in pairs_corrected]
# // store transformation, using a linear model as default
trafo_out = pyopenms.TransformationDescription()
trafo_out.setDataPoints(pairs_corrected)
model_params = pyopenms.Param()
model_params.setValue("symmetric_regression", 'false', '')
model_type = "linear"
trafo_out.fitModel(model_type, model_params)
return trafo_out
def test_run_mrmrtnormalizer(self):
# load chromatograms
chromatograms = pyopenms.MSExperiment()
fh = pyopenms.FileHandler()
fh.loadExperiment(self.chromatograms, chromatograms)
# load TraML file
targeted = pyopenms.TargetedExperiment()
tramlfile = pyopenms.TraMLFile()
tramlfile.load(self.tramlfile, targeted)
# Create empty files as input and finally as output
empty_swath = pyopenms.MSExperiment()
trafo = pyopenms.TransformationDescription()
output = pyopenms.FeatureMap()
# set up featurefinder and run
featurefinder = pyopenms.MRMFeatureFinderScoring()
# set the correct rt use values
scoring_params = pyopenms.MRMFeatureFinderScoring().getDefaults()
scoring_params.setValue("Scores:use_rt_score".encode(),
'false'.encode(), ''.encode())
featurefinder.setParameters(scoring_params)
featurefinder.pickExperiment(chromatograms, output, targeted, trafo,
empty_swath)
# get the pairs
pairs = []
simple_find_best_feature(output, pairs, targeted)
pairs_corrected = pyopenms.MRMRTNormalizer().removeOutliersIterative(
pairs, 0.95, 0.6, True, "iter_jackknife")
pairs_corrected = [list(p) for p in pairs_corrected]
expected = [(1497.56884765625, 1881.0), (2045.9776611328125, 2409.0),
(2151.4814453125, 2509.0), (1924.0750732421875, 2291.0),
(612.9832153320312, 990.0), (1086.2474365234375, 1470.0),
(1133.89404296875, 1519.0), (799.5291137695312, 1188.0),
(1397.1541748046875, 1765.0)]
for exp, res in zip(expected, pairs_corrected):
self.assertAlmostEqual(exp[0], res[0], eps)
self.assertAlmostEqual(exp[1], res[1], eps)
