Question

I posted a question before a week and the answer was simply (use join):

join <(sort file1) <(sort file2) >output

to join files that have something common which is usually the first field.

I have the following two files:

genes.txt

ENSG001 ENSG002
ENSG002 ENSG001
ENSG003 ENSG004

features.txt

ENSG001 400
ENSG002 350
ENSG003 210
ENSG004 100

I need to join these two files to be like this:

output.txt

ENSG001 400 ENSG002 350
ENSG002 350 ENSG001 400
ENSG003 210 ENSG004 100

I know the answer is in join command but I can’t figure out how to join based on two fields. I tried

join -j 1 <(sort genes.txt) <(sort features.txt) >attempt1.txt

but the result will looks like this:

attempt1.txt

ENSG001 ENSG002 400
ENSG002 ENSG001 350
ENSG003 ENSG004 210

I then tried

join -j 2 <(sort -k 2 genes.txt) <(sort -k 2 features.txt) >attempt2.txt

attempt2.txt is empty

Does (join) have the ability to join two files based on two fields ? If no then how can I do it ?

Answer 1

Thank you all guys I have managed to answer it by tricking the problem.

First I joined the files normally, I then changed the position of first and second field, I next joined the modified output file another time with features, and finally I switched the positions of fields again.

join <(sort genes.txt) <(sort features.txt) >tmp

cat tmp | awk '{ print $2, $1, $3 }' >tmp2

join <(sort tmp2) <(sort features.txt) >tmp3

cat tmp3 | awk '{ print $2, $3, $1, $4 }' >output.txt