Shell Programming and Scripting

@FCC189PACXX:2:1101:1420:2139/1
AGCGAGACTCCGTCTCAAAAAGAAAAAATTTTTCAAAATATTGCAATGGGCTTGTAATTTCTGCTTAAATGTCAGGAGGTCTGAGCCATT
+
bbbeeeceggggghiiiiiiiiiihfihihiiihhhghiihhihifhihiihhhhhhhhiiigfggggdceeeeebdcc^``bbcbccbb
@FCC189PACXX:2:1101:1368:2220/1
AGCTGTTGTCCTCCTCATTCTCGCAATCGCTGCAGTGCTCATGGCCGTTCCCGTTCCCTTCCATCATCTGCGGCAGCGGAGGTGCCCGCG
+
___eeceegacegeghihhdf`ggfhi`ebeWeccegcfdgihih_cceefcgghedf_\\`ddZbYZ^RZX`]^BBBBBBBBBBBBBBB
@FCC189PACXX:2:1101:2390:2054/1
NAAGTGGTAAATAATAAGCCTCCTGACTTGTGGTTGTAGCCTCATTTCTTGGTGTATGACAATTGACACTTCTGTAGAAAACCTGCTGGC
+
BP\cccecgggggiiiiiiiiiiiiiiiihhhhhiiiiiiiiihiiiiiiihgfhigiihiegifffhiiiiiehggggggddeeeddcc
@FCC189PACXX:2:1101:2484:2119/1
CAAAATCACTAAAATGCCCTGCCAGTCATTACAACCAGAACCAATAAACACCCCAACACACACAAAACAACAGTTGAAGGCATCCCTGGG
+
bbbeeeeeggggfiiiiiiiiiihifhihiiiihiihihiiihhiiiiiiiiifiiiiiiiigggeeeeccccddb`_bb`abccccc^a
@FCC189PACXX:2:1101:2450:2153/1
AAGCTTTCTTGAAATTAAGTATGTCATAACCTTCATTTCTGTTATGTGTAGCTGGCAGAGAGAGACAAGAATAAGAAACTTTGGAGGGCG
+
bbbeeeeegggggiiiiiiihihiiihiiiiiiiihiiiiihhhhihihhhiiihiihhihihhhhhiifghcbfdfggggggeedecba

@FCC189PACXX:2:1101:2450:2153/1
AAGCTTTCTTGAAATTAAGTATGTCATAACCTTCATTTCTGTTATGTGTAGCTGGCAGAGAGAGACAAGAATAAGAAACTTTGGAGGGCG
+
bbbeeeeegggggiiiiiiihihiiihiiiiiiiihiiiiihhhhihihhhiiihiihhihihhhhhiifghcbfdfggggggeedecba

sed 's/@/\x00/g' infile | shuf -z | sed 's/\x00/@/g' > outfile

shuf: memory exhausted

#!/usr/bin/perl
my $rsz = 216;
my $fsize = -s $ARGV[0];
my $record;

my @recs = (0..($fsize/$rsz)-1);

fisher_yates_shuffle(\@recs);

open(fp, $ARGV[0]) || die;
for (my $c = 0; $c < $#recs; $c++ ) {
        seek(fp, $recs[$c]*$rsz, 0);
        read(fp, $record, $rsz);
        print $record;
}
close(fp);

sub fisher_yates_shuffle {
    my $array = shift;
    my $i;
    for ($i = @$array; --$i; ) {
        my $j = int rand ($i+1);
        next if $i == $j;
        @$array[$i,$j] = @$array[$j,$i];
    }
}