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.