I have one program that is executed by a simple line written to the command line: 
>program -fFileToWriteTo FileToReadFrom

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and was wondering how to write a perl script to simply write this to the command line. (I can then get the results by reading in from the results file created, no problem.)

A second program, however, is executed from the command line and then asks for a filename to be entered: 

>coils
Please enter filename of sequence

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Does this require a different kind of script to write into a program?

For this program the results are displayed in the command line (as a list of letters amd probabilities) and not written to a file. How can i read them into my script?

Help on any of the above matters is appreciated, thanks

In reply to Command Line by Mahoota

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