sigprofiler issue

[ShixiangWang]

This was reported by Ziyu and a PR is waiting for this issue. @taoziyu97 Please push a PR at your spare time.

[taoziyu97]

Message received.
I‘m still debugging it by using SBS data.

[ShixiangWang]

Ok.

[taoziyu97]

使用SBS数据，CNV数据分别对调用SigProfilerExtractor的函数Sigprofiler.R进行反复调试发现

• 1.1.0版本中对于CNV 使用method = S 的48个分类（method = X的不会报错）会出现如下报错：

Traceback (most recent call last):
  File "/Users/taozy/Library/r-miniconda/envs/sigminer_sigprofiler/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3080, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 4554, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 4562, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'Mutation Types'

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

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/taozy/Library/r-miniconda/envs/sigminer_sigprofiler/lib/python3.7/site-packages/SigProfilerExtractor/sigpro.py", line 486, in sigProfilerExtractor
    data["Mutation Types"]= pd.Categorical(data["Mutation Types"], orderlist1)
  File "/Users/taozy/Library/r-miniconda/envs/sigminer_sigprofiler/lib/python3.7/site-packages/pandas/core/frame.py", line 3024, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/Users/taozy/Library/r-miniconda/envs/sigminer_sigprofiler/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3082, in get_loc
    raise KeyError(key) from err
KeyError: 'Mutation Types'

对sigprofiler.R中第102行代码：tibble::rownames_to_column("MutationType")修改为tibble::rownames_to_column("Mutation Types")后，能够顺利运行

• 1.1.3 版本中无论是SBS还是不同的CNV分类方法都不会报错。

• 经过调试总结：将MutationType改成Mutation Types在1.1.0和1.1.3版本中都不会报错，SBS和各类CNV都能够运行。

[ShixiangWang]

Got it.