I have a file that has a list of entries in a column

x
z
z
z
x
y
z

The column can have any length and any number of any strings. I need to replace each unique string with a user defined number. I can filter the unique entries out using

awk '{if (NF==5) print $2}' file | uniq | nl > list.tmp

which would give

1 x
2 y
3 z

I then want to ask the user 'what do you want to replace x with? what do you want to replace y with?' and so on. I then set up a loop to read each line in the file as a variable and loop over these and replace each one with the user input

Y=1
while [ $Y -le $Nspecies ]; do #Nspecies is 3 in this case
species=`grep "$Y" species.tmp | awk '{print $2}'` #pick species in turn
echo "Enter vibration amp. for species" $species #user defined replacement
read amp
sed s/"$species"/"$amp"/ speciesorder.txt >> $outfile #do switch replace
Y=$((Y+1))
done

This almost works, it loops over the species x,y,z and asks for input but it always overwrites x again and again and doesn't move onto the others. I think the problem lies in the sed substitution of a variable for a user defined variable.

I would really appreciate any mistakes you might have spotted or any other ways to do this you might think of.