CODEWITHSUNDEEP
shell
Deepti Jain
Deepti Jain

Reputation: 1921

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 

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 ?

Upvotes: 0

Views: 195

Answers (1)

jdigital
jdigital

Reputation: 12296

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.

Upvotes: 1

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