How to match two different length and different column text file with header using join command in linux

Question

I have two different length text files A.txt and B.txt

A.txt looks like:

ID  pos  val1  val2  val3
1   2    0.8     0.5   0.6
2   4    0.9     0.6   0.8
3   6    1.0     1.2   1.3
4   8    2.5     2.2   3.4
5   10   3.2     3.4   3.8

B.txt looks like:

pos category
2    A
4    B
6    A
8    C
10   B

I want to match pos column and in both files and want the output like this

ID  catgeory  pos  val1  val2  val3
1      A       2    0.8     0.5   0.6
2      B       4    0.9     0.6   0.8
3      A       6    1.0     1.2   1.3
4      C       8    2.5     2.2   3.4
5      B       10   3.2     3.4   3.8

I used the join function join -1 2 -2 1 <(sort -k2 A.txt) <(sort -k1 B.txt) > C.txt

The C.txt comes without a header

    1      A       2    0.8     0.5   0.6
    2      B       4    0.9     0.6   0.8
    3      A       6    1.0     1.2   1.3
    4      C       8    2.5     2.2   3.4
    5      B       10   3.2     3.4   3.8

I want to get output with a header from the join function. kindly help me out

Thanks in advance

Answer 1

In case you are ok with awk , could you please try following. Written and tested with shown samples in GNU awk .

awk 'FNR==NR{a[$1]=$2;next} ($2 in a){$2=a[$2] OFS $2} 1' B.txt A.txt | column -t

Explanation: Adding detailed explanation for above.

awk '                       ##Starting awk program from here.
FNR==NR{                    ##Checking condition FNR==NR which will be TRUE when B.txt is being read.
  a[$1]=$2                  ##Creating array a with index of 1st field and value is 2nd field of current line.
  next                      ##next will skip all further statements from here.
}
($2 in a){                  ##Checking condition if 2nd field is present in array a then do following.
  $2=a[$2] OFS $2           ##Adding array a value along with 2nd field in 2nd field as per output.
}
1                           ##1 will print current line.
' B.txt A.txt | column -t   ##Mentioning Input_file names and passing awk program output to column to make it look better.

Answer 2

As you requested... It is perfectly possible to get the desired output using just GNU join :

$ join -1 2 -2 1 <(sort -k2 -g A.txt)  <(sort -k1 -g B.txt) -o 1.1,2.2,1.2,1.3,1.4,1.5
ID category pos val1 val2 val3
1 A 2 0.8 0.5 0.6
2 B 4 0.9 0.6 0.8
3 A 6 1.0 1.2 1.3
4 C 8 2.5 2.2 3.4
5 B 10 3.2 3.4 3.8
$

The key to getting the correct output is using the sort -g option, and specifying the join output column order using the -o option.

To "pretty print" the output, pipe to column -t

$ join -1 2 -2 1 <(sort -k2 -g A.txt)  <(sort -k1 -g B.txt) -o 1.1,2.2,1.2,1.3,1.4,1.5 | column -t
ID  category  pos  val1  val2  val3
1   A         2    0.8   0.5   0.6
2   B         4    0.9   0.6   0.8
3   A         6    1.0   1.2   1.3
4   C         8    2.5   2.2   3.4
5   B         10   3.2   3.4   3.8
$