#!/usr/bin/perl -w
use warnings;
use strict;

my @desired_cols = qw(colname1 colname3);
my @desired_cols1= qw(colname3);
my $temp = 'tmp.txt';
# reads first line to get actual column names
open(S1, 'S1.txt') || die "Can't open S1: $!";
open(S2, 'S2.txt') || die "Can't open S2 : $!";
open(OUT, ">$temp") || die "Can't create output : $!"; 
my $header_line = (<S1>);
my $header_line1 = (<S2>);


my @actual_cols = split(/\s+/,$header_line);


# get column number of the actual column names

my $pos  =0;
my %col2_num = map {$_ => $pos++}@actual_cols;

# translate the desired col names into position numbers
                              
my @slice = map{$col2_num{$_}}@desired_cols;               
my @slice1 = map{$col2_num{$_}}@desired_cols1;

print OUT join("\t","@desired_cols"),"\r\n"; #header line
# print colname1 colname3 colname3 in outfile 


while (<S1>, <S2>)
{
  my @row = (split)[@slice];
  my @row1 = (split)[@slice1];
  print OUT join("\t","@row @row1"),"\r\n";       #each data row
  
}