Shell Programming and Scripting

        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

#!/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		 
   	 }