#!/user/bin/perl -w                                                                                                           
# Use your own path                                                                                                           
use strict; # always use strict                                                                                               
my $file = "josh_vamps_seqs_ALL.fa";
open (FILE, $file) or die "$0: $!"; # printing errors is a Good Thing (tm)                                                    
my @file = <FILE>; # Store all the lines in an array                                                                          
close FILE;

open OUT, ">rarefaction.fa" or die "$0: $!"; # Caution: will overwrite any existing files                                     
my $i;
for ($i = 0; $i<4266;$i++) { # Start sampling loop                                                                            
    my $rand = int(rand($#file));
# rand gives you a random number between 0 and the number of lines remaining in the array, note                               
# that this number is by necessity dynamic, it will drop 1000, 999, 998, etc.                                                 
    my $sample = splice @file, $rand, 1; # Cut out the $rand-th line, offset 1 means just one line                            
    print OUT $sample;
} # end of for loop