Shell Programming and Scripting

#!/usr/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: $!";
      while (<FH>) {
          chomp;
          if ($. == 1) {
              $final_header = sprintf("%s\t%s\t%s\n", join("\t", @left), $_, join("\t",@right));
              last;
          }
      }
      close (FH) or die "Can't close $input_file: $!";
    
      # Once the final header is set, print it to the output file
      open (FH, ">", $output_file) or die "Can't open $output_file: $!";
      print FH $final_header;
      close (FH) or die "Can't close $output_file: $!";

 open (FH, "<", $input_file) or die "Can't open $input_file: $!";

 
cd 'C:\Users\cmccabe\Desktop\annovar'
	 perl matrix.pl < "${id}".txt.hg19_multianno.txt > "L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_"${id}".txt"