Create a BED file of windows of any size from another BED file.

windowize-bed.pl

#Command: cat in.bed | perl windowize-bed.pl <windowsize> > out.bed
$windowsize=shift;
$ctr=0;
print STDERR "$ctr";
while($line=<STDIN>) {
    $ctr++;
    print STDERR "\r$ctr";
    chomp($line);
    @line=split(/\t/, $line);
    for($i=$line[1]; $i<$line[2]-$windowsize+1; $i+=$windowsize) {
        $end=$i+$windowsize;
        print STDOUT "$line[0]\t$i\t$end\n";
    }
}
print STDERR "\r$ctr\n";