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Thats the problem

tried using double slashes, still not resolved PermissionError Traceback (most recent call last) Cell In[17], line 1 ----> 1 sc.read_csv('G:\scanpy data\extracted\GSM5226574_C51ctr_raw_counts.csv').T

File ~\AppData\Local\Programs\Python\Python310\lib\site-packages\anndata_io\read.py:54, in read_csv(filename, delimiter, first_column_names, dtype) 30 def read_csv( 31 filename: Union[PathLike, Iterator[str]], 32 delimiter: Optional[str] = ",", 33 first_column_names: Optional[bool] = None, 34 dtype: str = "float32", 35 ) -> AnnData: 36 """
37 Read .csv file. 38 (...) 52 Numpy data type. 53 """ ---> 54 return read_text(filename, delimiter, first_column_names, dtype)

File ~\AppData\Local\Programs\Python\Python310\lib\site-packages\anndata_io\read.py:358, in read_text(filename, delimiter, first_column_names, dtype) 356 return _read_text(f, delimiter, first_column_names, dtype) 357 else: --> 358 with filename.open() as f: 359 return _read_text(f, delimiter, first_column_names, dtype)

File ~\AppData\Local\Programs\Python\Python310\lib\pathlib.py:1117, in Path.open(self, mode, buffering, encoding, errors, newline) 1115 if "b" not in mode: 1116 encoding = io.text_encoding(encoding) -> 1117 return self._accessor.open(self, mode, buffering, encoding, errors, 1118 newline)

PermissionError: [Errno 13] Permission denied: 'G:\scanpy data\extracted\GSM5226574_C51ctr_raw_counts.csv'

  • Does this answer your question? [PermissionError: \[Errno 13\] in Python](https://stackoverflow.com/questions/13207450/permissionerror-errno-13-in-python) – doneforaiur Jun 20 '23 at 11:42
  • Jupyter maybe cannot access that drive. It looks like your Jupyter is running elsewhere based on `~\AppData\Local\Programs\Python\Python310\lib\site-packages\anndata_io\read.py`. And so move the file to some place Jupyter can access and then try with that new path. See [answers to 'Open Jupyter Notebook from a Drive Other than C Drive'](https://stackoverflow.com/q/55078484/8508004). – Wayne Jun 20 '23 at 16:27

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