Read all files from a folder in the same directory
Files with the same name but different extension
On .txt extensions,count the number of words,the start and end offset of each word,output into a textfiles
Merge a1,a2,ann,rel(other file extensions),on read each line,and store it into a data-structure
Join results of 3,4 and output into a new folder <pre>_result
What are the operations that I can use to achieve this with CI?

CI can’t do all of this for you. You’re going to have to know some php or be willing to read the manual. See php.net for lots of info on how to work with php.