Randomise a BED file.

random_bed.pl

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <infile.bed>\n";
my $infile = shift or die $usage;

my %bed = ();

open(IN,'<',$infile) || die "Could not open $infile: $!\n";
while(<IN>){
   chomp;
   $bed{$.} = $_;
}
close(IN);

foreach my $line (keys %bed){
   print "$bed{$line}\n";
}

exit(0);