$
$ cat -n set_header.pl
     1  #!/usr/bin/perl
     2  use strict;
     3
     4  # Accept the input and output files as parameters
     5  my $input_file = $ARGV[0];
     6  my $output_file = $ARGV[1];
     7
     8  # Set the header columns to be added to the left
     9  # and to the right of the header in the input file
    10  my @left =  (
    11                   "Index",
    12                   "Chromosome Position",
    13                   "Gene",
    14                   "Inheritance",
    15                   "RNA Accession",
    16                   "Chr",
    17                   "Coverage",
    18                   "Score",
    19                   "A(#F,#R)",
    20                   "C(#F,#R)",
    21                   "G(#F,#R)",
    22                   "T(#F,#R)",
    23                   "Ins(#F,#R)",
    24                   "Del(#F,#R)",
    25                   "SNP db_xref",
    26                   "Mutation Call",
    27                   "Mutant Allele Frequency",
    28                   "Amino Acid Change"
    29              );
    30  my @right = (
    31                  "HP",
    32                  "SPLICE",
    33                  "Pseudogene",
    34                  "Classification",
    35                  "HGMD",
    36                  "Disease",
    37                  "Sanger",
    38                  "References"
    39              );
    40
    41  # Now open the input file, read the header line and sandwich it
    42  # between @left and @right arrays
    43  my $final_header;
    44  open (FH, "<", $input_file) or die "Can't open $input_file: $!";
    45  while (<FH>) {
    46      chomp;
    47      if ($. == 1) {
    48          $final_header = sprintf("%s\t%s\t%s\n", join("\t", @left), $_, join("\t",@right));
    49          last;
    50      }
    51  }
    52  close (FH) or die "Can't close $input_file: $!";
    53
    54  # Once the final header is set, print it to the output file
    55  open (FH, ">", $output_file) or die "Can't open $output_file: $!";
    56  print FH $final_header;
    57  close (FH) or die "Can't close $output_file: $!";
    58
$
$ perl set_header.pl del.txt.hg19_multianno.txt my_output.txt
$
$ sed 's/\t/\n/g' my_output.txt
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
Chr
Start
End
Ref
Alt
Func.refGene
Gene.refGene
GeneDetail.refGene
ExonicFunc.refGene
AAChange.refGene
PopFreqMax
1000G2012APR_ALL
1000G2012APR_AFR
1000G2012APR_AMR
1000G2012APR_ASN
1000G2012APR_EUR
ESP6500si_ALL
ESP6500si_AA
ESP6500si_EA
CG46
common
clinvar
clinvarsubmit
clinvarreference
Otherinfo
HP
SPLICE
Pseudogene
Classification
HGMD
Disease
Sanger
References
$
$