Shell Programming and Scripting

data=as.matrix(read.table("data.txt"))
file=as.matrix(read.table("file.txt"))
n1=dim(file)[1]    # number of lines in file.txt
n2=dim(data)[1]  # number of lines in data.txt
control=file[,3:4] # 3th and 4th column of file.txt
new=matrix(nrow=n1, ncol=1)  # new matrix to store the output
count=0
for (j in 1:n1)
{
 count=count+1
  for (i in 1:n2)
 {  
  if (data[i, ((2*j)-1):(2*j)]!=c(control[j,1],control[j,1])&& data[i, ((2*j)-1):(2*j)]!=c(control[j,1],control[j,2])&& data[i, ((2*j)-1):(2*j)]!=c(control[j,2],control[j,1])&& data[i, ((2*j)-1):(2*j)]!=c(control[j,2],control[j,2]))  
   {
    new[count]=file[j,1]
   }
  } 
}

#!/usr/bin/ksh
cut -d' ' -f1,2 data.txt > data2.txt
# Input for loop will be: G A snp1 265 G T
paste data2.txt file.txt |
while read m1 m2 m3 m4 m5 m6; do
  if [[ "${m1}" = "${m5}" && "${m2}" = "${m6}" ]]; then
    echo ${m3}
  fi
done