Python程序“genipe”类型错误：yu init_uu（）获得意外的关键字参数“normalize”

Question

我试着运行genipe程序来做一些全基因组生存分析。我已经安装了精灵和所有相关的目录。但是，当我运行程序时，我得到了一个错误：

“TypeError:init\uu（）获得意外的关键字参数”“normalize”“”

我没有编辑任何精灵脚本，我已经运行精灵没有问题，在另一个服务器，所以我不确定是什么出了问题！任何帮助都将不胜感激。在

非常感谢

卡拉格

编辑： 我使用的是python3.6.1版

回溯如下：

Traceback (most recent call last):
  File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
    return list(map(*args))
  File "/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 "/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 "/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 "/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 "/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 "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
    return list(map(*args))
  File "/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 "/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 "/users/k1640238/miniconda/envs/genipe_pyvenv/bin/imputed-stats", line 11, in <module>
    sys.exit(main())
  File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 161, in main
    options=args,
  File "/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 "/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 "/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

根据lifeline changelog判断，此关键字参数已从该特定函数中删除。生命线是一个包含这个特殊函数的包，它是used by genipe。在

您可以自己安装以前版本的生命线，看看是否有帮助，或者在genipe库中等待更新。在

再看看你的评论中的错误，它看起来像this is problematic code。您正在尝试使用dmatrices，但它似乎没有被定义。可能是因为前面提到的try/catch块找不到安装的statsmodel，因此{}也没有导入。在

尝试手动安装更多的包，从

• statsmodel
• patsy

看看你会不会有错误。。。在

Answer 2

看上面勘误表的答案，我使用了一些依赖关系的错误版本，但是即使这样，程序仍然给我错误。然而，当我恢复到Python3.4时，该程序工作了。在