LinuxQuestions.org - shell scripting for accepting input from different directories automatically

The two shell scripts (t1prog and t2prog) are given below they are working fine. The input for the first program is 't1.det' and for second program is 't1.rnaml'. These two input files are in 'dir1' folder. I am executing the shell like 'sh t1prog > t1out' and 'sh t2prog > t2out' from this directory only. Then I am executing a java program 'java RNA'; for this, t1out and t2out are input files used in the program and I am getting the final output on screen.

The input files 't1.det' and 't1.rnaml' are in different folders with same name and with different values. Each folder specifies one gene sequence input files.

In mfold directory there are 5 directors and each directory contains these input files as shown below
cd mfold
dir1 dir2 dir3 dir4 dir5
cd dir1
t1.det t1.rnaml
-----
cd dir5
t1.det t1.rnaml

I requesting you to please help me in shell script to automate this process like t1prog and t2prog first take the inputs from dir1 folder, run the shell and redirect the output to t1out and t2out and after executing the java program with statment 'java RNA' the output will be redirected to a file like 'RNAout1'. Then takes the inputs from dir2 folder, same process again, and redirect the output to 'RNAout2'. Like this for all inputs values from 5 folders. Modify the two shell scripts given below, to accept the inputs in that way.

shell 1: t1prog

1. #!/bin/bash
2. PrintVal() { C=${C#*(}; C=${C%)*}; echo $C | sed 's/).*( /-/'; }
3. while IFS=':=' read A B C
4. do
5. case $(echo $A) in
6. Initial*)
7. ((NotFirst)) && { echo; echo; } || NotFirst=1
8. echo ${B#* }; echo
9. Hairpins=0
10. ;;
11.
12. Hairpin*)
13. ((Hairpins==0)) && echo "$A:"
14. PrintVal
15. ((Hairpins++))
16. ;;
17. Multi-loop)
18. echo "$A:"
19. PrintVal
20. ;;
21. esac
22. done <t1.det

shell 2: t2prog

#!/bin/sh
i=1
while read line
do
freecount=`echo "${line}" | grep -i "free" | wc -l`
poscount=`echo "${line}" | grep -i "position" | wc -l`
if [ $freecount -eq 1 ]
then
rangeoutput=0
else
rangeoutput=1
fi
if [ $rangeoutput -eq 0 ]
then
value=`echo "${line}" | sed -n 's/<.*>$.*$<.*>/\1/p'`
echo $value
else
if [ $poscount -eq 1 ]
then
pvalue[$i]=`echo "${line}" | sed -n 's/<.*>$.*$<.*>/\1/p'`
if [ $i -eq 2 ]
then
echo "${pvalue[1]} - ${pvalue[2]}"
i=0
fi
i=`expr $i + 1`
fi
fi
done <t1.rnaml
-----------------------------
for one input in dir1 i am executing like this

sh t1prog > t1out
sh t2prog > t2out
java RNA

for inputs in different directories and executing these and redirecting the final ouput after executing 'java RNA' statement to a file is needed.
PLS. KINDLY HELP ME WHICH IS VERY ESSENTAIL FOR ME. THANKING YOU