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Automating execution of commands inside a program

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# 1  
Old 01-01-2012
Automating execution of commands inside a program
I have a program dnapars
I execute the program from command line as following:
./dnapars
The program then prompts me some message as a user menu from where I have to select a series of options in the order R U Y R. And then I copy the output file (outfile) in another result file.
I wrote the following script, but the execution hangs where it is supposed to execute the R option
Code:
    for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
    do
    cp ../../../EditDistanceRandomParsimonator/RAxML_parsimonyTree.test4D20RI$i.0 intree
    ./dnapars
    R      <----- This doesn't execute
    U
    Y
    R
    cp outfile result$i
    done

How can I make the script to run the options R U Y R under the dnapars program ?
Last edited by jim mcnamara; 01-02-2012 at 12:41 AM.. Reason: code tags please
# 2  
Old 01-02-2012
Quote:
Originally Posted by deeptisjains
for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
do
cp ../../../EditDistanceRandomParsimonator/RAxML_parsimonyTree.test4D20RI$i.0 intree
./dnapars
R <----- This doesn't execute
U
Y
R
cp outfile result$i
done
It won't work this way.

1. What is dnapars program? Is it another shell script?
2. Is so, why not modify dnapars to take in the 4 options (R U Y R) directly from command line as Positional Parameters?
# 3  
Old 01-02-2012
Try this:
Code:
   for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
    do
    cp ../../../EditDistanceRandomParsimonator/RAxML_parsimonyTree.test4D20RI$i.0 intree
    ./dnapars  <<EOF
R  
U
Y
R
EOF
    cp outfile result$i
    done

Note the last EOF is all the way over to the left. This is called a here document.
# 4  
Old 01-02-2012
Try this:
Code:
for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
    do
    cp ../../../EditDistanceRandomParsimonator/RAxML_parsimonyTree.test4D20RI$i.0 intree    
    echo "Enter Option"
    read option
    if [ "$option" == "R" ]
  then
   ./dnapars R
  fi
    
    echo "Enter Option"
    read option
    if [ "$option" == "U" ]
  then
   ./dnapars U
  fi
    
    # other options
    
    cp outfile result$i
    done


Moderator's Comments:
Mod Comment How to use code tags
Last edited by Franklin52; 01-02-2012 at 04:17 AM.. Reason: Please use code tags for code and data samples, thank you
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