!/usr/bin/perl
use strict;
use warnings;

my $col_file  = shift;
my $data_file = shift;

open my $columns, '<', $col_file 
    or die "Could not open $col_file - $!\n";

open my $file, '<', $col_file
    or die "Could not open $data_file - $!\n");

my @columns = split /\s+/, <$columns>;
chomp(@columns);

# use a hash for quick lookup of columns to skip
# here I use a hash slice to assign undef values to the keys stored in @columns
my %skip; @skip{@columns} = ();

while( my $line = <$file>) {
    chomp $line;
    my @raw_data = split /\s+/, $line;

    # Map and grep are a bit tough for newbies but they are important, powerful tools that should be mastered.
    # Read from right to left:
    # Take the list of indexes in @raw_data
    # (grep) keep only those that do not exist as keys to %skip
   # (map) and look up the the item at that index in @raw_data
   # and finally print the resulting list.

    print join ' ', 
          map $raw_data[$_], 
          grep !exists $skip{$_}, 0..$#raw_data;
    print "\n";

}