UNIX for Dummies Questions & Answers

$ cat merge.awk

BEGIN { FS="\t"; OFS="\t" }

NR==1 {
        print
        MAX=NF
        for(N=1; N<=NF; N++)    ORDER[$N]=N
        next
}

NR==FNR { D[$1]=$0; next }

# Pick up order of fields from second file
FNR==1 {
        for(N=1; N<=NF; N++)    REORDER[N]=ORDER[$N];
        next
}

$1 in D {
        print D[$1]
        for(N=2; N<=MAX; N++)
                printf("%s%s", OFS, $(REORDER[N]));
        printf("\n");
}

$ cat file1

gene    W       X       Y       Z
I       1       2       3       4
II      5       6       7       8
III     9       10      11      12
IV      13      14      15      16

# Note the altered column order
$ cat file2

gene    W       Y       X       Z
I       d1
II              a3
III     b1
IV                              c1

$ awk -f merge.awk file1 file2

gene    W       X       Y       Z
I       1       2       3       4
        d1
II      5       6       7       8
                        a3
III     9       10      11      12
        b1
IV      13      14      15      16
                                c1

$

 
 paste -d "|" file1 file2 | sed 's/|/\n/g' | tail -n +2