Python程序「genipe」 - TypeError：__init __（）得到了一個意想不到的關鍵字參數'正常化'

Question

我想運行程序genipe做一些全基因組生存分析。我已經安裝genipe和所有相關的目錄。然而，當我去運行程序出現錯誤：

「類型錯誤：_ 初始化 _（）得到了一個意想不到的關鍵字參數‘正常化’」

我沒有任何編輯的genipe的腳本和我運行genipe沒有問題在不同的服務器上，所以我不知道什麼是錯的！任何幫助將不勝感激。

非常感謝，

卡拉

編輯： 我使用Python 3.6.1版

回溯如下：

Traceback (most recent call last): 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 119, in worker 
    result = (True, func(*args, **kwds)) 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar 
    return list(map(*args)) 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 965, in process_impute2_site 
    use_ml=site_info.use_ml, 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 1048, in fit_cox 
    cf = CoxPHFitter(alpha=0.95, tie_method="Efron", normalize=False) 
TypeError: __init__() got an unexpected keyword argument 'normalize' 
""" 

The above exception was the direct cause of the following exception: 

Traceback (most recent call last): 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 811, in compute_statistics 
    for result in pool.map(process_impute2_site, sites_to_process): 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 260, in map 
    return self._map_async(func, iterable, mapstar, chunksize).get() 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 608, in get 
    raise self._value 
TypeError: __init__() got an unexpected keyword argument 'normalize' 

[2017-05-31 14:18:53 ERROR] __init__() got an unexpected keyword argument 'normalize' 
multiprocessing.pool.RemoteTraceback: 
""" 
Traceback (most recent call last): 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 119, in worker 
    result = (True, func(*args, **kwds)) 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar 
    return list(map(*args)) 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 965, in process_impute2_site 
    use_ml=site_info.use_ml, 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 1048, in fit_cox 
    cf = CoxPHFitter(alpha=0.95, tie_method="Efron", normalize=False) 
TypeError: __init__() got an unexpected keyword argument 'normalize' 
""" 

The above exception was the direct cause of the following exception: 

Traceback (most recent call last): 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/bin/imputed-stats", line 11, in <module> 
    sys.exit(main()) 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 161, in main 
    options=args, 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 811, in compute_statistics 
    for result in pool.map(process_impute2_site, sites_to_process): 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 260, in map 
    return self._map_async(func, iterable, mapstar, chunksize).get() 
    File "https://stackoverflow.com/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 608, in get 
    raise self._value 
TypeError: __init__() got an unexpected keyword argument 'normalize' 

Answer 1

由lifeline changelog這個關鍵字參數具有判斷已從此特定功能中刪除。生命線是一個包含這個特殊功能的包，並且是used by genipe。

你可以自己安裝以前版本的生命線，看看它是否有助於或等待genipe庫中的更新。

從您的評論中查看更多的錯誤，看起來好像是this is problematic code。您正嘗試使用dmatrices，但似乎沒有定義。可能是因爲提到try/catch塊找不到statsmodel安裝，因此也沒有導入patsy。

嘗試手動安裝其他軟件包，從

• statsmodel
• patsy

，看看你會得到任何錯誤，那麼......

Answer 2

見勘誤的答案在上面，我使用了一些依賴關係的錯誤版本，但即使如此，該程序仍然給我錯誤。但是當我恢復到python 3.4時，該程序起作用。