Hi, I wrote a script to compare values on two columns, but I only want to do this while the id on the 4th column remains the same. The file looks like this:

chr1      15865      15915      cg13869341      908      913
chr1      18827      18877      cg14008030      688      776
chr1      29407      29457      cg12045430      43      70
chr1      29407      29457      cg12045430      43      88
chr1      29407      29457      cg12045430      43      16
chr1      29425      29475      cg20826792      57      70
chr1      29425      29475      cg20826792      57      88
chr1      29425      29475      cg20826792      57      16
chr1      29435      29485      cg00381604      33      70
chr1      29435      29485      cg00381604      33      88
chr1      29435      29485      cg00381604      33      16
chr1      68849      68899      cg20253340      560      593
chr1      69591      69641      cg21870274      791      809
chr1      91550      91600      cg03130891      55      84
[download]

So for example I want to compare line 3,4,5 because they have the same id in column 4. My code looks like this now:

open(intersectMethyl,'<',"intersect148methyl.bed") or die $!;
my @methylData = <intersectMethyl>;
close(intersectMethyl);

my @methylScore;
my @ids;

for my $line(@methylData){
    my($chr,$start,$end,$id,$scoreNormal,$scoreTumor) = split("\t",$li
+ne);
    push(@ids, $id);
    for ($i = 1; $i<eof; $i++){
      if (@ids[$i]==@ids[$i-1] &&  (($scoreTumor/1000) - ($scoreNormal
+/1000) >= 0.2)){
        push(@methylscore, "$chr    $start    $end    $id    $scoreNor
+mal    $scoreTumor")
      }
    }
}


open(RESULTS,'>','methylDifferences.txt') or die $!;
foreach(@methylscore){
   print RESULTS "$_\n";
}
close(RESULTS);
[download]

But this doesn't work.. Could somebody help me? Thanks!

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