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GilbertLabUCSF / ScreenPro2

[This is an archived repository, see the current version in Arc Institute GitHub]
https://github.com/ArcInstitute/ScreenPro2
MIT License
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Error in "Collapsing transcript scores to gene scores" #3

Closed abearab closed 1 year ago

abearab commented 2 years ago 
Collapsing transcript scores to gene scores
Traceback (most recent call last):
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/abearab/Research/screenPro Project/ScreenPro2/screenpro/processing/scores.py", line 795, in <module>
    processExperimentsFromConfig(args.Config_File, args.Library_File_Directory, args.plot_extension.lower())
  File "/Users/abearab/Research/screenPro Project/ScreenPro2/screenpro/processing/scores.py", line 266, in processExperimentsFromConfig
    geneTableCollapsed = scoreGeneByBestTranscript(geneTable)
  File "/Users/abearab/Research/screenPro Project/ScreenPro2/screenpro/processing/scores.py", line 301, in scoreGeneByBestTranscript
    curFrame = geneTable.loc[zip(bestTranscriptFrame.index,bestTranscriptFrame[tup]),tup]
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__
    return self._getitem_tuple(key)
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple
    return self._getitem_lowerdim(tup)
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1373, in _getitem_lowerdim
    return self._getitem_nested_tuple(tup)
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1453, in _getitem_nested_tuple
    obj = getattr(obj, self.name)._getitem_axis(key, axis=axis)
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1954, in _getitem_axis
    return self._getitem_iterable(key, axis=axis)
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1595, in _getitem_iterable
    keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False)
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1552, in _get_listlike_indexer
    self._validate_read_indexer(
  File "/Users/abearab/anaconda3/envs/candi/lib/python3.8/site-packages/pandas/core/indexing.py", line 1640, in _validate_read_indexer
    raise KeyError(f"None of [{key}] are in the [{axis_name}]")
KeyError: "None of [MultiIndex([(       'A2M', nan),\n            (    'A4GALT', nan),\n            (      'AACS', nan),\n            (      'AATF', nan),\n            (     'ABCA1', nan),\n            (    'ABCA13', nan),\n            (     'ABCA3', nan),\n            (     'ABCA4', nan),\n            (     'ABCA5', nan),\n            (     'ABCA6', nan),\n            ...\n            ('pseudo_990', nan),\n            ('pseudo_991', nan),\n            ('pseudo_992', nan),\n            ('pseudo_993', nan),\n            ('pseudo_994', nan),\n            ('pseudo_995', nan),\n            ('pseudo_996', nan),\n            ('pseudo_997', nan),\n            ('pseudo_998', nan),\n            ('pseudo_999', nan)],\n           names=['gene', 'transcripts'], length=6040)] are in the [index]"