Pairwise matrix from a pandas dataframe

Question

I have a pandas dataframe that looks something like this:

             Al01   BBR60   CA07    NL219
AAEAMEVAT    MP      NaN     MP      MP 
AAFEDLRLL    NaN            


        

Answer 1

It just matrix multiplication:

import pandas as pd
df = pd.read_csv('data.csv',index_col=0, delim_whitespace=True)
df2 = df.applymap(lambda x: int(not pd.isnull(x)))
print df2.T.dot(df2)

Output:

           Al01  BBR60  CA07  NL219
Al01      4      0     2      3
BBR60     0      1     0      0
CA07      2      0     3      3
NL219     3      0     3      4

[4 rows x 4 columns]