How to concatenate specific rows in python?

Question

I am looking to learn how to concatenate multiple columns in python. I have a dataset which looks like this:

gene    match_type  drug                sources      pmids
ABO     Definite    CHEMBL50267         DrugBank     17139284|17016423
ABO     Definite    URIDINE_DIPHOSPHATE TdgClinicalTrial   17139284|17016423
ABO     Definite    CHEMBL439009        DrugBank     12972418
ABO     Definite    CHEMBL1232343       DrugBank       NA
ABO     Definite    CHEMBL503075        DrugBank       NA

I am trying to bring this into one row (concatenating the drug column, the sources column and the pmids column) to look like:

gene    match_type  drug                                                                         sources                                           pmids
ABO     Definite    CHEMBL1232343 CHEMBL439009 CHEMBL50267 CHEMBL503075 URIDINE_DIPHOSPHATE NA  DrugBank TdgClinicalTrial DrugBank DrugBank DrugBank    0 12972418 17139284|17016423  17139284|17016423 NA NA

I have looked into using if statements using pandas.concat and .iterrows to go through everything, but I have gotten a bit lost with this and I am not sure actually what functions I should have started with to achieve my goal. Any help in the right direction would be appreciated.

This is what I've tried but it's got a lot wrong it if not everything:

for index, row in data.iterrows():
    if[1,2]==[2,1]:
        pd.concat(['drug'],['interaction_types'],['sources'],['pmids'],)
    else: 
        print(row[:])

Done but I don't think I've done anything correctly, not sure where to start with getting pd.concat for only specific columns — DN1
– DN1, Commented Feb 18, 2019 at 11:40

Chris · Accepted Answer · 2019-02-18 11:52:07Z

1

Using pd.DataFrame.groupby and its agg:

joined_df = df.groupby(["gene", "match_type"]).agg(lambda x: ' '.join(x.astype(str))).reset_index()
print(joined_df)
  gene match_type                                               drug  
0  ABO   Definite  CHEMBL50267 URIDINE_DIPHOSPHATE CHEMBL439009 C...   

                                             sources
0  DrugBank TdgClinicalTrial DrugBank DrugBank Dr...   

                                               pmids  
0  17139284|17016423 17139284|17016423 12972418 n...

answered Feb 18, 2019 at 11:52

Chris

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