Add noise to simulated dataset

Author: zmzhang

python/FPIC.py

@@ -46,16 +46,20 @@ def plot_region(rg, rt = None, mz = None):
  show()
 
 def data2mzxml(path, converter = 'C:/Program Files/OpenMS/bin/FileConverter.exe'):
- files=os.listdir(path)
+ if os.path.isfile(path):
+ files = [path]
+ path = ""
+ elif os.path.isdir(path):
+ files=os.listdir(path)
  for f in files:
  if f.lower().endswith(".mzdata"): 
  file_in = path + f
  file_out = path + f[0:-6] + "mzxml"
- subprocess.Popen([converter, '-in', file_in, '-out', file_out])
+ subprocess.call([converter, '-in', file_in, '-out', file_out])
  if f.lower().endswith(".mzml"):
  file_in = path + f
  file_out = path + f[0:-4] + "mzxml"
- subprocess.Popen([converter, '-in', file_in, '-out', file_out]) 
+ subprocess.call([converter, '-in', file_in, '-out', file_out]) 
 
 
 def pics_id(pics, n):

python/LCMSSimulation.py

@@ -23,10 +23,13 @@ def simulation(fasta, contaminants, out, out_cntm,
 
  subprocess.call([simulator, '-in', fasta, '-out', out, '-out_cntm',out_cntm, 
  '-algorithm:MSSim:RawSignal:contaminants:file', contaminants,
+ '-algorithm:MSSim:RawSignal:noise:detector:stddev', '1',
+ '-algorithm:MSSim:RawSignal:resolution:value', '5000',
+ '-algorithm:MSSim:RawSignal:resolution:type', 'constant',
  '-algorithm:MSSim:Ionization:mz:lower_measurement_limit', '10',
  '-algorithm:MSSim:Ionization:mz:upper_measurement_limit', '1000',
  '-algorithm:MSSim:RT:total_gradient_time', '1000',
- '-algorithm:MSSim:RT:sampling_rate', '0.1',
+ '-algorithm:MSSim:RT:sampling_rate', '0.25',
  '-algorithm:MSSim:RT:scan_window:min', '0',
  '-algorithm:MSSim:RT:scan_window:max', '1000'])
 
@@ -148,22 +151,13 @@ def match_features(ground_truths, df):
  subprocess.call([peak_picker,'-in', 'MM48_MSS_Profile.mzML',
  '-out', 'MM48_MSS.mzML'])
 
- data2mzxml('./')
+ data2mzxml('MM48_MSS.mzML')
 
  ground_truths = parse_featureXML_GT('MM48_MSS.featureXML')
 
  mzfile = "MM48_MSS.mzxml"
  mzMLfile = "MM48_MSS.mzML"
 
- tic()
- parser=mzXMLParser()
- lcms = parser.parseFile(mzfile.encode(sys.getfilesystemencoding()))
- pics_c = pm.FPICs(lcms, 10.0, 200.0, 0.5)
- toc()
- 
- match_fpic = ground_truths.copy()
- match_features(match_fpic, pics2df(pics_c))
- match_fpic.detected.value_counts()
 
  tic()
  feature_map = FeatureFindingMetabo(mzMLfile)
@@ -183,5 +177,15 @@ def match_features(ground_truths, df):
  match_xcms = ground_truths.copy()
  match_features(match_xcms, df_xcms)
  match_xcms.detected.value_counts()
+ 
+ tic()
+ parser=mzXMLParser()
+ lcms = parser.parseFile(mzfile.encode(sys.getfilesystemencoding()))
+ pics_c = pm.FPICs(lcms, 10.0, 200.0, 0.5)
+ toc()
+ match_fpic = ground_truths.copy()
+ df_fpic = pics2df(pics_c)
+ match_features(match_fpic, df_fpic)
+ match_fpic.detected.value_counts()