The empty row in the print you see is because the index
has a name - Gene.name
(This is not a real row in the DataFrame though) . If you don't want that row , I believe you would need to do away with the name. Example -
df.index.name = None
Demo -
In [6]: df = pd.DataFrame([[1,2,3,4],[1,2,3,4]]).set_index(0)
In [7]: df
Out[7]:
1 2 3
0 <-------------------------- Name of the index for this DataFrame
1 2 3 4
1 2 3 4
In [10]: df.index.name=None
In [11]: df
Out[11]:
1 2 3
1 2 3 4
1 2 3 4
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