Code:
$ cat file
c1,c2,C3,c4,c5,c6
r1,r2,r3,r4,r5,r6
p1,p2,p3,p4,p5,p6,p7
w1,w2,w3,w4,w5,w6
y1,y2,y3,y4,y5,y6
z1,z2,z3,z4,z5,z6
c1,c2,C3,c4,c5,c6
r1,r2,r3,r4,r5,r6,r7,r8
p1,p2,p3,p4,p5,p6
w1,w2,w3,w4,w5,w6
y1,y2,y3,y4,y5,y6
z1,z2,z3,z4,z5,z6
$ awk -F, '{for(i=1;i<=NF;i++){A[NR,i]=$i};if(NF>n){n=NF}}
END{for(i=1;i<=n;i++){
s=A[1,i]?A[1,i]:" ";
for(j=2;j<=NR;j++){
p=A[j,i]?A[j,i]:" "
s=s","p}
print s}}' file
c1,r1,p1,w1,y1,z1,c1,r1,p1,w1,y1,z1
c2,r2,p2,w2,y2,z2,c2,r2,p2,w2,y2,z2
C3,r3,p3,w3,y3,z3,C3,r3,p3,w3,y3,z3
c4,r4,p4,w4,y4,z4,c4,r4,p4,w4,y4,z4
c5,r5,p5,w5,y5,z5,c5,r5,p5,w5,y5,z5
c6,r6,p6,w6,y6,z6,c6,r6,p6,w6,y6,z6
, ,p7, , , , ,r7, , , ,
, , , , , , ,r8, , , ,