在 Jupyter Notebook 中读取 .pkl 文件时出现 pyranges 模块错误

Question

我需要读取 JupyterLab 中的 .pkl 文件。我的代码是：

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

得到的错误是：

---------------------------------------------------------------------------
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'

我尝试卸载然后安装 pyranges 模块。我已经在 JupyterLab 中安装了 pyranges。

我已确保模块路径包含在系统路径中：

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']

我也尝试使用

dill

，而不是

pickle

：

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

即便如此，我也遇到了同样的错误：

/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'

我没有使用 python 及其包、模块、内核等等的经验。我现在只需要读取 .pkl 文件。对我来说，这似乎是模块“pyranges”的问题。我已经尝试了迄今为止基于此找到的解决方案。

Answer 1

我也有同样的问题。安装 pyranges==0.0.129 解决了这个问题