input_parse_and_output("Note");

# Subroutine has two arguments 1.Input file name 2. Output file direct
+ory 3. Output file name all of these are scalar

sub input_parse_and_output{
 foreach my $input_data_each_line(@input_data_in_array){
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Please explain how these four lines fit together. The documentation does not fit the call of the function. Passed parameters do not fit the documentation. The passed parameters never get used in the code.

You seem to be highly confused about what goes where in Perl code. Please post a complete, runnable example of your program which has the problem you have but which is shorter than 20 lines.