I'd be thrilled to hear what you're trying to do - it's always a challenge to see if there IS a way to do it in Splunk after all (there often is) 🙂
I believe what you want is to run an alert action. Schedule the search for the data you want sent to the script. Make an alert action that runs a script. The arguments are sent to the script and you can parse it at will from there.
http://docs.splunk.com/Documentation/Splunk/5.0/Alert/Setupalertactions#Run_a_script
I want to make some report, which I am not able to make through the commands available in splunk, that's y want to write a perl script so that its output can be my desired result ..
Please give more information. What do you want to execute and when? Are you looking to implement a custom search command or do you want to use a script when an alert triggers, or something else entirely?