Shell Programming and Scripting

my @colsleft = map "Null",(1..$#left);	  
	   my @colsright = map "Null",(0..$#right);	 
	  	  
	  while(<FH>)  {  # puts row of input file into $_ 
	  chomp;
	  my @vals = split/\t/; # this splits the line at tabs
	  my @mutations=split/,/,$vals[9]; # splits on comma to create an array of mutations
	  my ($gene,$transcript,$exon,$coding,$aa);
	  for (@mutations)
	  {	
			($gene,$transcript,$exon,$coding,$aa) = split/\:/; # this takes col AB and splits it at colons
			grep {$transcript eq $_} keys %nms or next;
		}
		# warn join ("\t",$gene,$transcript,$exon,$coding,$aa);
		my @out=($.,@colsleft,$_,@colsright);
		$out[2]=$gene;
		$out[3]=$nms{$transcript};
		$out[4]=$transcript;
		$out[15]=$coding;
		$out[17]=$aa;
		$out[45]="VUS";

 #!/bin/perl
   use strict;
   my %nms=("NM_004004.5"=>"AR","NM_004992.3"=>"XLD","NM_003924.3"=>"AD");  # match NM and inheritence with gene
    
 # 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 $_ 
   chomp;
   my @vals = split/\t/; # this splits the line at tabs
   my @mutations=split/,/,$vals[9]; # splits on comma to create an array of mutations
   my ($gene,$transcript,$exon,$coding,$aa);
   for (@mutations)
   { 
   ($gene,$transcript,$exon,$coding,$aa) = split/\:/; # this takes col AB and splits it at colons
    grep {$transcript eq $_} keys %nms or next;
  }
  # warn join ("\t",$gene,$transcript,$exon,$coding,$aa);
  my $classification = "VUS";
  my @out=($.,@colsleft,$_,@colsright);
  $out[2]=$gene;
  $out[3]=$nms{$transcript};
  $out[4]=$transcript;
  $out[15]=$coding;
  $out[17]=$aa;
  $out[45]=$classification;
  
  #print OF join("\t",$.,@colsleft,$_,@colsright),"\n";   # row data is set, print it to the output file  
  print OF join("\t",@out),"\n";   # row data is set, print it to the output file   
     }

push @out, "VUS";

my @out=($., @colsleft, $_, @colsright, "VUS");

$out[45] = "VUS";
print "$out[45]\n";

my @colsleft = map "null",(1..$#left);
my @colsright = map "null",(0..$#right);

perl -MData::Dumper -e '@a[2] = "Third element of a"; @a[10]="Eleventh element of a"; END{print Dumper \@a}'

$VAR1 = [
          undef,
          undef,
          'Third element of a',
          undef,
          undef,
          undef,
          undef,
          undef,
          undef,
          undef,
          'Eleventh element of a'
        ];

    for (@mutations) {
            ($gene,$transcript,$exon,$coding,$aa) = split/\:/; # this takes col AB and splits it at colons
            grep {$transcript eq $_} keys %nms or next;
    }

grep {$transcript eq $_} keys %nms or next;

   $out[2]=$gene;
    $out[3]=$nms{$transcript};
    $out[4]=$transcript;
    $out[15]=$coding;
    $out[17]=$aa;
    $out[45]=$classification;