shell scripting

["SENTHIL KUMAR" <nucleic81@gmail.com>]

Hi,
      i plan to run  a program over some 20 files were i need to input
one files as REFERENCE and then the remaining as TEST.  i have return
a script to  take every file in the list to be taken a REF and the
remaining as TEST and it works well{all with all }. but i want to
specify which one to be taken as reference so it wil  reduce my output
time and space . pls help me out  to rite a script. the lists of 20
files is in "list1" and the program is align.exe. "test.cor and
test.show" are the output files.
----------------------
#!/bin/sh

sed 's/.pdb//' list1 > temp_list1
total_files=`awk 'END {print NR}' list1`
echo "1" > temp1
echo "yes" >> temp1
echo "" > temp3
echo "" > temp5
echo "n" >> temp5
echo "auto" >> temp5
echo "test.cor" >> temp5
echo "test.show" >> temp5
count1=1
while [ $count1 -lt $total_files ]; do
        echo "count1=$count1"
        file_ref=`sed -n ''$count1'p' list1`
        new_ref=`sed -n ''$count1'p' temp_list1`
        echo $file_ref > temp2
        count2=`expr $count1 + 1`
        while [ $count2 -le $total_files ]; do
        echo "count2=$count2"
                file_work=`sed -n ''$count2'p' list1`
                new_work=`sed -n ''$count2'p' temp_list1`
                echo $file_work > temp4
                cat temp1 temp2 temp3 temp4 temp5 > align.in
                ./align.exe < align.in
                mv test.cor ${new_work}_${new_ref}.cor
                mv test.show ${new_work}_${new_ref}.show
                count2=`expr $count2 + 1`
        done
        count1=`expr $count1 + 1`
done
rm -f temp? temp_list1
--------------------------------------------