KeyError: 'False: boolean label can not be used without a boolean index'

[zhoushican]

%%time
adata=ov.pp.qc(adata,
              tresh={'mito_perc': 0.2, 'nUMIs': 500, 'detected_genes': 250},
              batch_key=None)
adata

When I run this line of code, the following error occurs：

{
	"name": "KeyError",
	"message": "'False: boolean label can not be used without a boolean index'",
	"stack": "---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File <timed exec>:1

File ~/mambaforge/envs/omicverse_gpuOne/lib/python3.10/site-packages/omicverse/pp/_qc.py:195, in qc(adata, **kwargs)
    193 if settings.mode == 'gpu':
    194     print('GPU mode activated')
--> 195     return qc_gpu(adata,**kwargs)
    196 else:
    197     print('CPU mode activated')

File ~/mambaforge/envs/omicverse_gpuOne/lib/python3.10/site-packages/omicverse/pp/_qc.py:464, in qc_gpu(adata, mode, min_cells, min_genes, nmads, max_cells_ratio, max_genes_ratio, batch_key, doublets, doublets_method, path_viz, tresh, mt_startswith, mt_genes)
    462 # QC plot
    463 QC_test = (adata.obs['passing_mt']) & (adata.obs['passing_nUMIs']) & (adata.obs['passing_ngenes'])
--> 464 removed = QC_test.loc[lambda x : x is False]
    465 removed_cells.extend(list(removed.index.values))
    466 print(f'Total cell filtered out with this last --mode {mode} QC (and its chosen options): \\
    467 {n1-np.sum(QC_test)}')

File ~/mambaforge/envs/omicverse_gpuOne/lib/python3.10/site-packages/pandas/core/indexing.py:1073, in _LocationIndexer.__getitem__(self, key)
   1070 axis = self.axis or 0
   1072 maybe_callable = com.apply_if_callable(key, self.obj)
-> 1073 return self._getitem_axis(maybe_callable, axis=axis)

File ~/mambaforge/envs/omicverse_gpuOne/lib/python3.10/site-packages/pandas/core/indexing.py:1311, in _LocIndexer._getitem_axis(self, key, axis)
   1308         return self.obj.iloc[tuple(indexer)]
   1310 # fall thru to straight lookup
-> 1311 self._validate_key(key, axis)
   1312 return self._get_label(key, axis=axis)

File ~/mambaforge/envs/omicverse_gpuOne/lib/python3.10/site-packages/pandas/core/indexing.py:1118, in _LocIndexer._validate_key(self, key, axis)
   1108 @doc(_LocationIndexer._validate_key)
   1109 def _validate_key(self, key, axis: int):
   1110     # valid for a collection of labels (we check their presence later)
   1111     # slice of labels (where start-end in labels)
   1112     # slice of integers (only if in the labels)
   1113     # boolean not in slice and with boolean index
   1114     if isinstance(key, bool) and not (
   1115         is_bool_dtype(self.obj._get_axis(axis))
   1116         or self.obj._get_axis(axis).dtype.name == \"boolean\"
   1117     ):
-> 1118         raise KeyError(
   1119             f\"{key}: boolean label can not be used without a boolean index\"
   1120         )
   1122     if isinstance(key, slice) and (
   1123         isinstance(key.start, bool) or isinstance(key.stop, bool)
   1124     ):
   1125         raise TypeError(f\"{key}: boolean values can not be used in a slice\")

KeyError: 'False: boolean label can not be used without a boolean index'"
}

[HendricksJudy]

Sir, after testing the specific script

Fix the KeyError in the qc_gpu function by correctly handling boolean labels.

• Update line 464 in qc_gpu function in omicverse/pp/_qc.py to use a boolean index instead of a boolean label.

  • Change removed = QC_test.loc[lambda x : x is False] to removed = QC_test.loc[QC_test == False].

  You may apply this to fix until the next update to solve this ERROR