GPL16304_450K_trim.pl

use Cwd;
use strict;
my $GPL16304=shift @ARGV;
open F, $GPL16304 || die "cannot open $GPL16304\n";
#print "CHR\tStart\tEnd\tcg\tgene\tstrand\tcpgisland\tprobetype\n";
while(<F>){
        next if /^#/;
        next if /Name/i;
        my @line=split/\t/;
        my $chr= $line[11];
        my $start=$line[12];
        my $end=$line[12]+1;
        my $cg=$line[0];
        my $strand=$line[16];
        my $gene=$line[21];
        my $cpgisland=$line[25];
        my $probetype=$line[6];
        $gene="NA" if $gene eq "";
        $cpgisland="CpG_Ocean" if $cpgisland eq "";
        ($gene,undef)=split/\;/,$gene;
        print "chr$chr\t$start\t$end\t$cg\t$gene\t$strand\t$cpgisland\t$probetype\n";

}

# usage
# perl GPL16304.pl GPL13534_450K_hg19_11288.txt > GPL13534_450K_hg19.bed