Python pandas: replace values multiple columns matching multiple columns from another dataframe

Question

I searched a lot for an answer, the closest question was Compare 2 columns of 2 different pandas dataframes, if the same insert 1 into the other in Python, but the answer to

Answer 1

You can use the update function (requires setting the matching criteria to index). I've modified your sample data to allow some mismatch.

# your data
# =====================
# df1 pos is modified from 10020 to 10010
print(df1)

   chr      snp  x    pos a1 a2
0    1  1-10020  0  10010  G  A
1    1  1-10056  0  10056  C  G
2    1  1-10108  0  10108  C  G
3    1  1-10109  0  10109  C  G
4    1  1-10139  0  10139  C  T

print(df2)

            ID  CHR   STOP  OCHR  OSTOP
0  rs376643643    1  10040     1  10020
1  rs373328635    1  10066     1  10056
2   rs62651026    1  10208     1  10108
3  rs376007522    1  10209     1  10109
4  rs368469931    3  30247     1  10139

# processing
# ==========================
# set matching columns to multi-level index
x1 = df1.set_index(['chr', 'pos'])['snp']
x2 = df2.set_index(['OCHR', 'OSTOP'])['ID']
# call update function, this is inplace
x1.update(x2)
# replace the values in original df1
df1['snp'] = x1.values
print(df1)

   chr          snp  x    pos a1 a2
0    1      1-10020  0  10010  G  A
1    1  rs373328635  0  10056  C  G
2    1   rs62651026  0  10108  C  G
3    1  rs376007522  0  10109  C  G
4    1  rs368469931  0  10139  C  T