ModuleError with pyranges when reading .pkl file in Jupyter Notebook

Question

I need to read a .pkl file in JupyterLab. The code I have is:

import dill
# Loading scplus_obj 
scplus_obj = dill.load(open('/path-to-my-file/scplus_obj.pkl', 'rb'))

The error get is :

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[12], line 2
      1 # Loading scplus_obj 
----> 2 scplus_obj = dill.load(open('/path-to-my-file/scplus_obj.pkl', 'rb'))

File ~/.local/lib/python3.8/site-packages/dill/_dill.py:287, in load(file, ignore, **kwds)
    281 def load(file, ignore=None, **kwds):
    282     """
    283     Unpickle an object from a file.
    284 
    285     See :func:`loads` for keyword arguments.
    286     """
--> 287     return Unpickler(file, ignore=ignore, **kwds).load()

File ~/.local/lib/python3.8/site-packages/dill/_dill.py:442, in Unpickler.load(self)
    441 def load(self): #NOTE: if settings change, need to update attributes
--> 442     obj = StockUnpickler.load(self)
    443     if type(obj).__module__ == getattr(_main_module, '__name__', '__main__'):
    444         if not self._ignore:
    445             # point obj class to main

File ~/.local/lib/python3.8/site-packages/dill/_dill.py:432, in Unpickler.find_class(self, module, name)
    430     return type(None) #XXX: special case: NoneType missing
    431 if module == 'dill.dill': module = 'dill._dill'
--> 432 return StockUnpickler.find_class(self, module, name)

ModuleNotFoundError: No module named 'pyranges.pyranges'

I have tried uninstalling then installing pyranges module. I have installed pyranges in the JupyterLab.

I have made sure the module path is included in the system paths:

import pyranges
print(pyranges.__file__)
import sys
sys.path

/home/cbgm/.local/lib/python3.8/site-packages/pyranges/__init__.py
['/home/cbgm/.local/lib/python3.8/site-packages/ray/thirdparty_files',
 '/home/cbgm',
 '/usr/lib/python38.zip',
 '/usr/lib/python3.8',
 '/usr/lib/python3.8/lib-dynload',
 '',
 '/home/cbgm/.local/lib/python3.8/site-packages',
 '/home/cbgm/scenicplus/src',
 '/usr/local/lib/python3.8/dist-packages',
 '/usr/lib/python3/dist-packages']

Instead of dill, I tried with pickle as well:

import pickle
with open('/path-to-my-file/scplus_obj.pkl', 'rb') as scplus_obj:
    data = pickle.load(scplus_obj)

Even then I get the same error:

/usr/lib/python3/dist-packages/paramiko/transport.py:219: CryptographyDeprecationWarning: Blowfish has been deprecated
  "class": algorithms.Blowfish,
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 3
      1 import pickle
      2 with open('/media/cbgm/6e648ddc-311d-4572-ac67-f8a548f153d4/Neel/Shuchun Li/70_SCENICplus_outs/01_Data/scenicplus/scplus_obj.pkl', 'rb') as scplus_obj:
----> 3     data = pickle.load(scplus_obj)

ModuleNotFoundError: No module named 'pyranges.pyranges'

I do not have experience with python and its packages, modules, kernels and all that. I just need to read the .pkl file in for now. To me it seems like an issue the module 'pyranges'. I have tried the solutions I have found so far based on that.

Answer 1

I had the same issue. Install pyranges==0.0.129 solved this issue