Using Awk to join two files based on several columns

I was reading a thread on stackoverflow and found this post very interesting. I will go through the problem and the awk solution. Again, Awk is awesome!

I created some dummy files.
file_a is a tab-delimited bed file with 5 colums:

file_b is the file that contain additional infomation, which we want to add to file_a:

we want to annotate file_a based on the fact that columns 3,4,5 in file_b are the same as columns 1,2,3 in file_a.
To do this, we are going to use Awk associated array. see a link

Let me execute the awk one-liner first and then explain what's going on here:

we annotated file_a using file_b. Aka, we added first two columns from file_b to file_a.
There are several things happening here:
we see built-in variables in awk: NR and FNR. NR is the line number of the current processing line.
when awk read in multiple files, awk NR variable will give the total number of records relative to all the input file. Awk FNR will give you number of records for each input file. see a link here for all the built-in variables in awk.
Let's deomonstrate the difference between NR and FNR:

FILENAME is another built-in variable for the input file name of awk. There are 4 lines in file_a and 2 lines in file_b, and NR increments for the total lines.
compare with FNR:

Now, awk prints out the line numbers in respect to each file.

From the awk code, we are reading file_b first. NR==FNR means when NR equals to FNR (this is true only for file_b) do the following: {a[$3,$4,$5]=$1OFS$2;next}. We created an associated array named a using columns 3,4,5 in file_b as keys and the columns 1 and 2: $1"\t"$2 as values. we set OFS="\t" in the end of the command. next means to proceed for the next line, rather than execute the following { } code block.

when awk reads in the second file (file_a.bed), NR==FNR is not true, awk exectues the second { } code block: {$6=a[$1,$2,$3];print}
we look up the associated array a we created from file_b.bed using the first three columns in file_a.bed as keys, and assign column 6 to the looked-up values and print it out the whole line.

Conclusion: Awk is very powerful in text wrangling. Once get used to the syntax, you can do fairly complicated formatting in an awk one-liner. I strongly recommand you to learn it.