Update perl code with parser

Shell Programming and Scripting
1

The below perl code imports the data in the attached document. However, I can not seem to update the perl code to include a parser like in the desired tab of that document. Thank you :).

Most of the data for the parse is included in the document except for the gene and RNA which can is hard-coded based on the text in bold:

  1. column AB (AAChange.refGene)has the Mutation (column p), and AminoAcid (column R) information in it
  2. the clinvar column (AN) has the information for classification (column AT) in it (first letter needs to be capital)
        column                D                E
If GJB2 then RNA = NM_004004.5 and Inheritance = AR

If MECP2 then RNA = NM_004992.3 and Inheritance = XLD

If PHOX2B then RNA = NM_003924.3 and Inheritance = AD

perl:

#!/bin/perl
   use strict;
     
       # Accept the input and output files as parameters
       my $input_file = $ARGV[0];
       my $output_file = $ARGV[1];
     
       # Set the header columns to be added to the left
       # and to the right of the header in the input file
      my @left =  (
                       "Index",
                       "Chromosome Position",
                       "Gene",
                       "Inheritance",
                       "RNA Accession",
                       "Chr",
                       "Coverage",
                       "Score",
                       "A(#F,#R)",
                       "C(#F,#R)",
                       "G(#F,#R)",
                       "T(#F,#R)",
                       "Ins(#F,#R)",
                       "Del(#F,#R)",
                       "SNP db_xref",
                       "Mutation Call",
                       "Mutant Allele Frequency",
                       "Amino Acid Change"
                  );
      my @right = (
                      "HP",
                      "SPLICE",
                      "Pseudogene",
                      "Classification",
                      "HGMD",
                      "Disease",
                      "Sanger",
                      "References"
                  );
    
      # open the input file, read the header line and sandwich it
      # between @left and @right arrays
      my $final_header;
      open (FH, "<", $input_file) or die "Can't open $input_file: $!";
	  chomp(my $hdr=<FH>);

      $final_header = sprintf("%s\t%s\t%s\n", join("\t", @left), $hdr, join("\t",@right));

      # final header is set, print it to the output file
      open (OF, ">", $output_file) or die "Can't open $output_file: $!";
      print OF "$final_header";
     # close (FH) or die "Can't close $output_file: $!";
	  
	   my @colsleft = map "Null",(1..$#left);	  
	   my @colsright = map "Null",(0..$#right);	 
	  	  
	  while(<FH>)  {  # puts row of input file into $_ 
	  chomp;
		print OF join("\t",$.,@colsleft,$_,@colsright),"\n";   # row data is set, print it to the output file		 
   	 }