Shell Programming and Scripting

perl my_program.pl < my_file.txt

perl my_program.pl my_file.txt

 
while (<FH>) {
          chomp;
          if ($. == 1) {
        }
}

 
while (my $row = <FH>) {
      chomp $row; }
      }
}

while (my $row = <FH>) {
      chomp $row; }
      }
}

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: $!";
	  
	  	  
	  # capture data
	  my $row_data;
	  open (RD, "<", $input_file) or die "Could not open $input_file: $!";

while( my $line = <RD>)  {   
    print $line;    
    last if $. == 2;
}

 
 perl matrix.pl del.txt.hg19_multianno.txt L:/NGS/3_BUSINESS/Matrix/Torrent/matrix_del.txt
Chr     Start   End     Ref     Alt     Func.refGene    Gene.refGene    GeneDetail.refGene      ExonicFunc.refGene      AAChange.refGene        PopFreqMax     1000G2012APR_ALL 1000G2012APR_AFR        1000G2012APR_AMR        1000G2012APR_ASN1000G2012APR_EUR        ESP6500si_ALL   ESP6500si_AA    ESP6500si_EA    CG46   common   clinvar clinvarsubmit   clinvarreference        Otherinfo
13      20763686        20763686        C       -       exonic  GJB2           frameshift deletion      GJB2:NM_004004.5:exon2:c.35delG:p.G12fs 0.011   .      ..       .       .       0.0074  0.0009  0.011   .

while we loop through each line of the file
begin
    -  if this is line 1 then
           do something for the header
    -  otherwise
          do something else for the data
end