Shell – How to merge two files in the same row

You can use paste for this:

paste -d '\0' aaaa.txt bbbb.txt > cccc.txt

From your question, it appears that the first file contains ; at the end. If it didn't, you could use that as the delimiter by using -d ';' instead.

Note that contrary to what one may think, with -d '\0', it's not pasting with a NUL character as the delimiter, but with an empty delimiter. That is the standard way to specify an empty delimiter. Some paste implementations like GNU paste allow paste -d '' for that, but it's neither standard nor portable (many other implementations will report an error about the missing delimiter if you use paste -d '').

This should do it:

join -j 2 -o 1.1,1.2,1.3,2.3 file1 file2

Important: this assumes your files are sorted (as in your example) according to the SNP name. If they are not, sort them first:

join -j 2 -o 1.1,1.2,1.3,2.3 <(sort -k2 file1) <(sort -k2 file2)

Output:

0 AFFX-SNP-000541 NA 1
0 AFFX-SNP-002255 NA 1
1 rs12103 0.6401 0.5596
1 rs12103_1247494 0.696 0.5581
1 rs12142199 0.7672 0.4931

Explanation (from info join):

`join' writes to standard output a line for each pair of input lines that have identical join fields.

`-1 FIELD'
     Join on field FIELD (a positive integer) of file 1.

`-2 FIELD'
     Join on field FIELD (a positive integer) of file 2.

`-j FIELD'
     Equivalent to `-1 FIELD -2 FIELD'.

`-o FIELD-LIST'

 Otherwise, construct each output line according to the format in
 FIELD-LIST.  Each element in FIELD-LIST is either the single
 character `0' or has the form M.N where the file number, M, is `1'
 or `2' and N is a positive field number.

So, the command above joins the files on the second field and prints the 1st,2nd and 3rd field of file one, followed by the 3rd field of file2.