Shell Programming and Scripting

A1	B1	A2	B2
0	0	1	1
1	0	0	1
0	1	1	0
1	1	1	1

label	A1	B1	A2	B2	
A1	2	1	1	2
B1	1	2	2	1
A2	1	2	3	2
B2	2	1	2	3

awk '
NR==1           {for (i=1; i<=NF; i++) HD[i]=$i
                 if (MXNF < NF) MXNF=NF
                 next
                }
                {L=NR-1
                 for (i=1; i<=NF; i++) VAL[i,L]=$i
                }

END             {for (i=1; i<=MXNF; i++)
                   for (j=1; j<=MXNF; j++)
                      for (l=1; l<=L; l++)
                        RES[i,j]+=(VAL[i,l]*VAL[j,l]) 


                 printf "Label\t"
                 for (h in HD) printf "%s\t", HD[h]
                 printf "\n"
                 for (i=1; i<=MXNF; i++)
                        {printf "%s\t", HD[i]
                         for (j=1; j<=MXNF; j++)
                                printf "%s\t", RES[i,j]
                         printf "\n"
                        }
                }
' file
Label    A1    B1    A2    B2    
A1    2    1    1    2    
B1    1    2    2    1    
A2    1    2    3    2    
B2    2    1    2    3

0       0       1       1
1       0       0       1
0       1       1       0
1       1       1       1

BEGIN {
  OFS="\t"
}
function calc(x,y,  i,comm) {
   for(i=1;i<=fnr;i++)
     if (a[i,x] && a[i,y]) comm++
   return(comm)
}

{ for(i=1;i<=NF;i++) a[FNR,i]=$i;nf=NF;fnr=FNR }
END {
  for(i=1; i <= fnr; i++)
    for(j=1;j<=nf;j++)
       printf("%s%d%s", (j==1)?"":OFS,calc(i,j),(j==nf)?ORS:"")
}