wow, thanks a lot, i shortened it significantly, 

sub readdt2 {
  my $ifn = shift;
  open(my $IFH, "<$ifn") or die "cannot open file $ifn\n";
  my $line;
  my @nt = ("A","C","G","T");
  my %ret;
  my @tmp;
  for my $j(@nt) {
    $ret{$j} = [];
    $line = <$IFH>;
    chomp($line);
    @tmp = split(/\s+/,$line);
    for (my $i=0; $i<=$#tmp; $i++ ) {
      $ret{$j}[$i]= $tmp[$i] +0.0001;
    }
  }
  close($IFH);
  return(\%ret);
}

[download]

but when i used a data dumper the numbers didnt add up to 1.00, "A" added up to 1.11, "T" added up to 1.04, "C" added up to .93, G added up to .92 does anything stick out to you?

In reply to Re^2: trouble understanding boss's code by DanielM0412
in thread trouble understanding boss's code by DanielM0412

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