python - Reading a file with pandas and use correlation coefficients on two columns
问题描述
I have a file like following with no header
0.000000 0.330001 0.280120
1.000000 0.355590 0.298581
2.000000 0.305945 0.280231
I want to read this file using pandas dataframe and want to perform correlation coefficient between the second and the third column.
I am trying like following:
import pandas as pd
df = pd.read_csv('COLVAR_hbondnohead', header=None)
df['1'].corr(df['2'])
It pops up with a huge error message. Am I not treating the columns properly? Any suggestion or hint?
Error message
Traceback (most recent call last):
File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 958, in pandas._libs.hashtable.Int64HashTable.get_item
TypeError: an integer is required
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3063, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 164, in pandas._libs.index.IndexEngine.get_loc
KeyError: '1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 958, in pandas._libs.hashtable.Int64HashTable.get_item
TypeError: an integer is required
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/frame.py", line 2685, in __getitem__
return self._getitem_column(key)
File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/frame.py", line 2692, in _getitem_column
return self._get_item_cache(key)
File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/generic.py", line 2486, in _get_item_cache
values = self._data.get(item)
File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/internals.py", line 4115, in get
loc = self.items.get_loc(item)
File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3065, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 164, in pandas._libs.index.IndexEngine.get_loc
KeyError: '1'
解决方案
Roy what is the file extension? is it .csv ? if it is you should add it to the end of fileName like pd.read_csv('COLVAR_hbondnohead.csv', header=None)
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