using awk to select lines in file A, based on finding matches in file B

Question

I have two files, file A looks like this:

1       101427      GENE|ACT-A      1       101589      GENE|ACT-B    0.0357
1       101427      GENE|ACT-A      1          


        

Answer 1

awk 'FNR == NR {keys[$1]; next} $3 in keys || $6 in keys' fileB fileA

Answer 2

I would use the awk solution as it only has to examine each file once, but here's an alternative.

{ join -1 3 <(sort -k3 fileA) <(sort fileB) 
  join -1 6 <(sort -k6 fileA) <(sort fileB)
} > output