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all the possible combinations between the values that have the same ID value

March 15, 2022

I have an input pd dataframe with two columns, one is the sequence and the second is an ID (it is a number between 1-1000). I want to get all the possible combinations between the sequences that have the same ID.

Input:

sequence    ID
CASSSTGVLLYEQCF 1
CASSSTGVLLYEQYF 1
CAFNAGGTSHGKLTF 2
CAFNAGGTSYGKLTF 2
CAINAGGTSYGKLTF 2
CANSPSPVAGTDTQYF    3
CASSPSPVAGTDTQYF    3

desired output

CASSSTGVLLYEQCF CASSSTGVLLYEQYF
CAFNAGGTSHGKLTF CAFNAGGTSYGKLTF
CAFNAGGTSYGKLTF CAINAGGTSYGKLTF
CAINAGGTSYGKLTF CAFNAGGTSHGKLTF
CANSPSPVAGTDTQYF    CASSPSPVAGTDTQYF

I have been reading into itertools but this only gives me all possible combinations without using the ID. Does anyone know how this can be done using python or has any tips for me where I can look?

>Solution :

Use custom lambda function with itertools.combinations per groups in GroupBy.apply:

from  itertools import combinations

df1 = df.groupby('ID')['sequence'].apply(lambda x: pd.DataFrame(combinations(x, 2), 
                                                               columns=['a','b']))
print (df1)
                     a                 b
ID                                      
1  0   CASSSTGVLLYEQCF   CASSSTGVLLYEQYF
2  0   CAFNAGGTSHGKLTF   CAFNAGGTSYGKLTF
   1   CAFNAGGTSHGKLTF   CAINAGGTSYGKLTF
   2   CAFNAGGTSYGKLTF   CAINAGGTSYGKLTF
3  0  CANSPSPVAGTDTQYF  CASSPSPVAGTDTQYF


df1 = df1.droplevel(1).reset_index()
print (df1)
   ID                 a                 b
0   1   CASSSTGVLLYEQCF   CASSSTGVLLYEQYF
1   2   CAFNAGGTSHGKLTF   CAFNAGGTSYGKLTF
2   2   CAFNAGGTSHGKLTF   CAINAGGTSYGKLTF
3   2   CAFNAGGTSYGKLTF   CAINAGGTSYGKLTF
4   3  CANSPSPVAGTDTQYF  CASSPSPVAGTDTQYF