Merge Two files of columns but insert columns of second file into columns of first file

You can use a loop in awk, for example

paste file_A file_B | awk '{     half = NF/2;     for(i = 1; i < half; i++)    {        printf("%s %s ", $i, $(i+half));    }    printf("%s %s\n", $half, $NF);}'

or

paste file_A file_B | awk '{     i = 1; j = NF/2 + 1;    while(j < NF)    {        printf("%s %s ", $i, $j);        i++; j++;    }    printf("%s %s\n", $i, $j);}'

The code assumes that the number of columns in awk's input is even.

Use this Perl one-liner after paste to print alternating columns:

paste file_A file_B | perl -F'\t' -lane 'print join "\t", @F[ map { ( $_, $_ + ( @F/2 ) ) } 0 .. ( $#F - 1 ) /  2 ];'

Example:

Create tab-delimited input files:

perl -le 'print join "\t", 1..5 for 1..2;' > file_Aperl -le 'print join "\t", "A".."E" for 1..2;' > file_Bhead file_A file_B

Prints:

==> file_A <==1       2       3       4       51       2       3       4       5==> file_B <==A       B       C       D       EA       B       C       D       E

Paste files side by side, also tab-delimited:

paste file_A file_B | perl -F'\t' -lane 'print join "\t", @F[ map { ( $_, $_ + ( @F/2 ) ) } 0 .. ( $#F - 1 ) /  2 ];'

Prints:

1       A       2       B       3       C       4       D       5       E1       A       2       B       3       C       4       D       5       E

The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-n : Loop over the input one line at a time, assigning it to $_ by default.
-l : Strip the input line separator ("\n" on *NIX by default) before executing the code in-line, and append it when printing.
-a : Split $_ into array @F on whitespace or on the regex specified in -F option.
-F'/\t/' : Split into @F on TAB, rather than on whitespace.

$#F : last index of the array @F with the input fields, split on tab.
0 .. ( $#F - 1 ) / 2 : array of indexes of the array @F, from the start (0) to half of the array. These are all indexes that correspond to file_A.
map { ( $_, $_ + ( @F/2 ) ) } 0 .. ( $#F - 1 ) / 2 : map takes the above array of indexes from 0 to half of the length of @F, and returns a new array, with twice the number of elements. Its elements alternate: (a) the index corresponding to file_A ($_) and (b) that index plus half the length of the array ($_ + ( @F/2 )), which is the corresponding index from file_B.
@F[ map { ( $_, $_ + ( @F/2 ) ) } 0 .. ( $#F - 1 ) / 2 ] : a slice of array @F with the specified indexes, namely alternating fields from file_A and file_B.

SEE ALSO:

perldoc perlrun: how to execute the Perl interpreter: command line switches
perldoc perldata: Slices

With one awk script parsing the files:

FNR==NR {    rec[NR] = $0    next}{    split(rec[FNR], fields)    for (i=1;i<=NF;i++) $i = fields[i] FS $i    print}

Usage:

awk -f tst.awk file_A file_B