Automating execution of commands inside a program

Question

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

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 ?

Can you not provide arguments to dnapars to control it? If not, do you have the source? If so, add argument parsing. If not, can you go back to the author and request it? Now you know why people don't always like interactive programs like that. One option if you need interactive input is to have an interactive program prompt for the information needed and then pass that information to the non-interactive program so that you don't always have to interact with the main computational code. This works well for many, but not all, programs. — Jonathan Leffler
– Jonathan Leffler, Commented Jan 2, 2012 at 4:49

jdigital · Accepted Answer · 2012-01-02 04:25:43Z

1

You may be able to use a shell here document, for example:

./dnapars <<EndOfOptions
R
U
Y
R
EndOfOptions

This will generally work if the program reads its options from stdin.

answered Jan 2, 2012 at 4:25

jdigital

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