Hi I have a bit of a snag with my perl code. I am trying to take a random unique sampling of a file containing >100,000 sequences. But right now the way the data is listed I can't seem to figure out how to write a good code.

What I have so far.....>

#!/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 rem
+aining in the array, note                               
# that this number is by necessity dynamic, it will drop 1000, 999, 99
+8, 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
[download]

What it gives me ......>

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
[download]

What I actually want .........>

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
[download]

What input file looks like ......>

>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
[download]

I don't know if there is a way for the random function of perl to recognize a specific piece of the input say the ">" and then print the line that follows? Any pointers would be greatly appreciated.>