file 1 
col0    col1 col2 col3 col4 col5 ... ...
samp1
samp2
samp3
samp4
....

files follow similar format and what i need to do is extract 1st and 4th column from the first file and output on a new file and then take out only 4th column from the rest of the files. 

So before i work on my actual project, i wanted to try with more simple table. The table i'm working on right now is 

S1.txt

col1	col2	col3
1	4	7
2	5	8
3	6	9

S2.txt

col1	col2	col3
1	44	77
2	55	88
3	66	99

The result i'm getting

col1	col3	col3
1	4	
2	5	
3	6

The result i want 

col1	col3	col3
1	4	77
2	5	88
3	6	99


##</code><code>##

 
#!/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
  
}