awk - need help comparing 2 files

[akhattri]

I have two files for which I want to compare first 2 columns. What I need is if col1 & 2 of file 1 matches col 1 & 2 of file 2, print that line of file 2.

File 1:
chr1 1 A
chr1 2 T
chr1 3 C

File 2:
chr1 2 Y
chr1 3 R
chr1 4 Q
chr2 5 R

output:
chr1 4 Q
chr2 5 R


I know in awk I can compare the two columns and print the matching lines in output but somehow the intersection does not work. The command that I use is:

awk 'NR==FNR { a[$1"\t"$2]=$3 } NR>FNR { k=$1"\t"$2; if (k in a) print $0}' file1 file2

[bioBob]

I do something like this in an awk script (modified for your scenario--but not tested):

#!/usr/bin/env gawk
###needs file 1 and file 2 as input, keeps from file 2 anything found in file 1
###awk -f (this file) file1 file2

####change fields to reflect the selection feilds as appropriate
BEGIN {
file1 = ARGV[1]
file2 = ARGV[2]

delete hash

while (getline < file1) {
hash[$1"_"$2] = 1
}

while (getline < file2) {
k=$1"_"$2
if (k in hash ==1) {
print $0
}
}

exit (0)
}

[lh3]

awk 'BEGIN{while((getline<"file1")>0)l[$1","$2]=1}!l[$1","$2]' file2