CpGI.format.pl

 #!/usr/bin/perl

 #creat CpGI shore region according to CpGI.bed
 #build CpGI, CpG shore and CpG Shelf.
 # remove CpG shores and CpG shelf overlapped with CpGIs.
 # bedtools intersect -v -a CpGSF.hg19.bed4 -b CpGI.hg19.bed > CpGSF.hg19.bed5
 
 use strict;
 use Cwd;
 my $dir=getcwd;
 chdir $dir or die "can't change into $dir\n";
 my $output=">CpGISF.hg19.bed4";
 my $input="CpGI.hg19.bed4";

 open F,"$input";
 open OUT,"$output";
 while(<F>){
 my ($chr,$start,$end,undef,undef)=split /\t/;

 my $shelfup=$start-4000;
 my $shelfdown=$end+4000;

 my $shoreup=$start-2000;
 my $shoredown=$end+2000;

 my $id1="$chr:$shelfup-$shoreup:CpG_Shelf_N";
 my $id2="$chr:$shoreup-$start:CpG_Shore_N";
 my $id3="$chr:$end-$shoredown:CpG_Shore_S";
 my $id4="$chr:$shoredown-$shelfdown:CpG_Shelf_S";
 my $id="$chr:$start-$end:CpGI";

 print OUT "$chr\t$shelfup\t$shoreup\t$id1\n";
 print OUT "$chr\t$shoreup\t$start\t$id2\n";
 print OUT "$chr\t$start\t$end\t$id\n";
 print OUT "$chr\t$end\t$shoredown\t$id3\n";
 print OUT "$chr\t$shoredown\t$shelfdown\t$id4\n";

 }