I have two Input files.

File1:

s2/80 20 . A T 86 F=5;U=4 s2/20 10 . G T 90 F=5;U=4 s2/90 60 . C G 30 F=5;U=4 

File2:

s2/90 60 . G G 97 F=5;U=4 s2/80 20 . A A 20 F=5;U=4 s2/15 11 . A A 22 F=5;U=4 s2/90 21 . C C 82 F=5;U=4 s2/20 10 . G . 99 F=5;U=4 s2/80 10 . T G 11 F=5;U=4 s2/90 60 . G T 55 F=5;U=4 

Expected Output:

s2/80 20 . A T 86 F=5;U=4 s2/80 20 . A A 20 F=5;U=4 s2/20 10 . G T 90 F=5;U=4 s2/20 10 . G . 99 F=5;U=4 

Logic: I want all the lines from File1 and File2 concatenated in the Output file: Conditions: If Column 1, 2, 4 of File1 and File2 exactly match and if Column 5 of File2 has a dot ie "." or if it match exactly with Column 4 of file2.

Code: I tried using the script:

BEGIN{} FNR==NR{ k=$1" "$2 a[k]=$4" "$5 b[k]=$0 c[k]=$4 d[k]=$5 next } { k=$1" "$2 lc=c[k] ld=d[k] # file1 file2 if ((k in a) && ($4==$5) && (lc==$4)) print b[k]" "$0 } 

But I get an Output of:

s2/80 20 . A T 86 F=5;U=4 s2/80 20 . A A 20 F=5;U=4 

Whereas My output should be:

s2/80 20 . A T 86 F=5;U=4 s2/80 20 . A A 20 F=5;U=4 s2/20 10 . G T 90 F=5;U=4 s2/20 10 . G . 99 F=5;U=4 

I would appreciate your help. Thanks.