#!/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                                                                                                           

##</code><code>##

CTTTTCTTCGGACTACTTACAAGGTGTTGCATGGTCGTC
>FW4WBAJ01DVAX5.ICM_PML_Bv6.PML_43_2003_06_09
CGAGTCAACGCGCAGAACCTTACCAACACTTGACATGTTCGTCGCGACTCTAAGAGATTA
TCTCTATGCGCAACGCGAAAACCTTACCTGGCCTTGACATGCATCTCTAAGCGTGTGAAA
>FMS0R7002J2YH1.ICM_CAM_Bv6.CAM_0011_2000_03_26
TGGTGCCTTCGGGAACGCAGTGACAGGTGATGCATGG
AAACCCTCAGAGACTTCGGTTAATGACATGTTTACAGGTGATGCATGGCCGTCG
>E6SXMJY02I00IR.ICM_BMO_Bv6.BMO_0005_2007_09_22
TTCGGTTCGGCCGGACGAAACACAGGTGT
TAGTGCGACGCGAAGAACCTTACCAGGGCTTAAATGTAGTGGGACAGGTCTAGAGATAGA
GGGTGCCCTTCGGGGAATCTAGTGAGAGGTGTTGCATGGCCGTCG
GTGAGCAACGCGCAGAACCTTACCAACCCTTGACATCCTGTGCTACTACCAGAGATGGTA
TACATCTACGCGAAGAACCTTATCTACACTTGACATACAGAGAACTTACCAGAGATGGTT
TGGTGCCTTCGGGAATCTAGTGACAGGTGATGCATGGCTGTCG
CACACCAACGCGAAAAACCTTACCAACACTTGACATGTTCGTCGCGACTCTAAGAGATTA
TTCGGTTCGGCCGGACGAAACACAGGTGTTGCATGGCTGTC

##</code><code>##

FW4WBAJ01DVAX5.ICM_PML_Bv6.PML_43_2003_06_09
FMS0R7002J2YH1.ICM_CAM_Bv6.CAM_0011_2000_03_26
E6SXMJY02I00IR.ICM_BMO_Bv6.BMO_0005_2007_09_22

##</code><code>##

>FRZPY5Q02F00L9.ICM_AWP_Bv6.AWP_0001_2007_08_23
ACTGCCAACGCGCAGAACCTTACCAGGTCCTGACTTCCTGACTATGGTTATTAGAAATAA
TTTCCTTCAGTTCGGCTGGGTCAGTGACAGGTGATGCATGGCCGTC
>FRZPY5Q02F00U8.ICM_AWP_Bv6.AWP_0001_2007_08_23
ACTGCCTAACCGATGAACCTTACCTACACTTGACATGCAGAGAACTTTCCAGAGATGGAT
TGGTGCCTTCGGGAACTCTGACACAGGTGATGCATCGCCGTC
>FRZPY5Q02F01NC.ICM_AWP_Bv6.AWP_0001_2007_08_23
ACTGCCTACGCGAAGAACCTTACCTACACTTGACATACAGAGAACTTACCAGAGATGGTT
TGGTGCCTTCGGGAACTCTGATACAGGTGATGCATGGCTGTC
>FRZPY5Q02F023C.ICM_AWP_Bv6.AWP_0001_2007_08_23
ACTGCCAACGCGCAGAACCTTACCAACCCTTGACATCCAGAGAATTTTCTAGAGATAGAT
TTGTGCCTTCGGGAACTCTGTGACAGGTGATGCATGGCTGTC