properly join two files based on 2 columns in common

Question

I have two files I\'m trying to join/merge based on columns 1 and 2. They look something like this, with file1 (58210 lin

Answer 1

awk 'NR==FNR{a[$1,$2]=$3;next} ($1,$2) in a{print $0, a[$1,$2]}' file1 file2

Look:

$ cat file1
2L      5753   33158
2L      8813   33158
2L      7885   33159
2L      1279   33159
2L      5095   33158
$
$ cat file2
2L      8813    0.6    1.2
2L      5762    0.4    0.5
2L      1279    0.5    0.9
$
$ awk 'NR==FNR{a[$1,$2]=$3;next} ($1,$2) in a{print $0, a[$1,$2]}' file1 file2
2L      8813    0.6    1.2 33158
2L      1279    0.5    0.9 33159
$

If that's not what you want, please clarify and perhaps post some more representative sample input/output.

Commented version of the above code to provide requested explanation:

awk ' # START SCRIPT

# IF the number of records read so far across all files is equal
#    to the number of records read so far in the current file, a
#    condition which can only be true for the first file read, THEN 
NR==FNR {

   # populate array "a" such that the value indexed by the first
   # 2 fields from this record in file1 is the value of the third
   # field from the first file.
   a[$1,$2]=$3

   # Move on to the next record so we don't do any processing intended
   # for records from the second file. This is like an "else" for the
   # NR==FNR condition.
   next

} # END THEN

# We only reach this part of the code if the above condition is false,
# i.e. if the current record is from file2, not from file1.

# IF the array index constructed from the first 2 fields of the current
#    record exist in array a, as would occur if these same values existed
#    in file1, THEN
($1,$2) in a {

   # print the current record from file2 followed by the value from file1
   # that occurred at field 3 of the record that had the same values for
   # field 1 and field 2 in file1 as the current record from file2.
   print $0, a[$1,$2]

} # END THEN

' file1 file2 # END SCRIPT

Hope that helps.