Python程序“genipe” - TypeError：__init __（）得到了一个意想不到的关键字参数'正常化'

Question

我想运行程序genipe做一些全基因组生存分析。我已经安装genipe和所有相关的目录。然而，当我去运行程序出现错误：

“类型错误：_ 初始化 _（）得到了一个意想不到的关键字参数‘正常化’”

我没有任何编辑的genipe的脚本和我运行genipe没有问题在不同的服务器上，所以我不知道什么是错的！任何帮助将不胜感激。

非常感谢，

卡拉

编辑： 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这个关键字参数具有判断已从此特定功能中删除。生命线是一个包含这个特殊功能的包，并且是used by genipe。

你可以自己安装以前版本的生命线，看看它是否有助于或等待genipe库中的更新。

从您的评论中查看更多的错误，看起来好像是this is problematic code。您正尝试使用dmatrices，但似乎没有定义。可能是因为提到try/catch块找不到statsmodel安装，因此也没有导入patsy。

尝试手动安装其他软件包，从

• statsmodel
• patsy

，看看你会得到任何错误，那么......

Answer 2

见勘误的答案在上面，我使用了一些依赖关系的错误版本，但即使如此，该程序仍然给我错误。但是当我恢复到python 3.4时，该程序起作用。