peakfilter issue

[rromoli]

Hi, this is the first time I use LipidFinder. I read the guide and following the steps you suggested. Running peakfilter I get this error:

$ python3 ~/.local/bin/run_peakfilter.py -i ~/Data/2021/lipidi/out_lipid_xcms_pos.csv -o results -p ~/Data/2021/lipidi/lipid.json
Traceback (most recent call last):##########------------| 66.7% Completed
File "/home/cism/.local/bin/run_peakfilter.py", line 10, in <module> sys.exit(main())

File "/home/cism/.local/lib/python3.7/site-packages/LipidFinder/run_peakfilter.py", line 51, in main
    PeakFilter.peak_filter(data, parameters, dst, args.verbose)

File "/home/cism/.local/lib/python3.7/site-packages/LipidFinder/PeakFilter/__init__.py", line 212, in peak_filter
  BroadContaminant.process_all_features(data, parameters)

File "/home/cism/.local/lib/python3.7/site-packages/LipidFinder/PeakFilter/BroadContaminant.py", line 52, in process_all_features
  __process_feature__, rtArray=rtArray, parameters=parameters)

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 894, in apply
  result = self._python_apply_general(f, self._selected_obj)

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 928, in _python_apply_general
  keys, values, mutated = self.grouper.apply(f, data, self.axis)

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/groupby/ops.py", line 238, in apply
  res = f(group)

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 878, in f
  return func(g, *args, **kwargs)

File "/home/cism/.local/lib/python3.7/site-packages/LipidFinder/PeakFilter/BroadContaminant.py", line 78, in __process_feature__
  parameters=parameters)

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/frame.py", line 7765, in apply
  return op.get_result()

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/apply.py", line 185, in get_result
  return self.apply_standard()

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/apply.py", line 276, in apply_standard
  results, res_index = self.apply_series_generator()

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/apply.py", line 290, in apply_series_generator
  results[i] = self.f(v)

File "/home/cism/.local/lib/python3.7/site-packages/pandas/core/apply.py", line 110, in f
  return func(x, *args, **kwds)

File "/home/cism/.local/lib/python3.7/site-packages/LipidFinder/PeakFilter/BroadContaminant.py", line 94, in __process_sample_mean__
  nonZeroIndex = intensities.to_numpy().nonzero()[0]
AttributeError: 'numpy.ndarray' object has no attribute 'to_numpy'`

While I have a good knowledge of R language, I am a newbie in Python so I'm not able to solve the issue I get running the code. Can you help me to fix it?

[JAlvarezJarreta]

Hello @rromoli, we have recently discovered some bugs regarding BroadContaminant that have been addressed (and involved the lines your error is reporting) and will be included in the release binary 2.0.2 that is now available. Please, give it a try and don't hesitate to reach back if the issue perseveres.