Thanks guys, I have figured it out, my program is now running. You guys are great

And would you like to share your solution so others may follow and learn from your experience?

It was a matter of putting everything in a loop

#!/bin/bash
f1="goy 45 1 1"
file="/home/con/gen"
i=0
while read line; do
echo $f1 > $i
echo $line >> $i
cat $i
./perm
i=$(($i+1))
done <filename

It was just understanding how the loop works. It was starring me in the face. Thanks