my  $countref = ($t[8] =~ tr/.,//);
          my $ratioo = $countref/$t[7] ;

        if ($countref/$t[7] >0.95)  {
#       print "$t[1]\t$t[2]\t$t[3]: $ratioo \n";
       $seq .=$t[2];


        }
     elsif ($countref/$t[7] <=0.95){

         $t[8] =~ s/[.,]/$t[2]/g;

        my  $counta = ($t[8] =~ tr/aA//);
        my  $countt = ($t[8] =~ tr/tT//);
        my  $countg = ($t[8] =~ tr/gG//);
        my  $countc = ($t[8] =~ tr/cC//);

        my ($ratioa, $ratiot, $ratiog, $ratioc, $rat);
        my @rat = ();

        $ratioa = $counta/$t[7];
        $ratiot = $countt/$t[7];
        $ratiog = $countg/$t[7];
        $ratioc = $countc/$t[7];

print " $t[1] : A $ratioa T $ratiot G $ratiog C $ratioc ";
my      $rrat = \@rat;
         push (@rat, "$ratioa", "$ratiot", "$ratiog", "$ratioc");

         my $countnut = 0;
         my $i;
         my @ncode;
         my $ccode;
    for $i(0..$#rat){
        if ( $rrat->[$i]  >= 0.05){
            $i++;
          push (@ncode, $i);
         $countnut ++;
            $i--;
            }
            $ccode = join ("", @ncode);

        if ($countnut >= 3) {
#          print "N\n"; 
            $seq .= "N";
            }

#print " code:$ccode count $countnut\n"; 
     else {
     my   %hash;
       %hash = {1, 'A',
                 2,  'T',
                 3,  'G',
                 4,  'C',
                 12, 'W',
                 21, 'W',
                 13, 'R',
                 31, 'R',
                 14, 'M',
                 41, 'M',
                 23, 'K',
                 32, 'K',
                 24,  'Y',
                 42, 'Y',
            };

              print "cc", $hash{$ccode},"\n" ;

         }
  }

}
[download]

Like the other monks, I don't have a clue what your goals really are. (Try using shorter sentences when explaining things.) I took your code and data as posted, and put them together into a single file like this:

#!/usr/bin/perl

while (<DATA>) {
    next if (/^#/ or /^\s*$/);
    chomp;
    @t = split /\t/;
# your code goes here
}

__DATA__
# your data goes here
[download]

(update: I initially forgot to mention "split")

I had to edit the data to make it tab-delimited -- maybe the tabs were converted to spaces because of the way you posted it (or the way I downloaded it), but you may need to check and make sure whether your file really has the right number of tabs per line.

Anyway, your code ran and produced output with no errors. So what's the problem? If you were expecting some different sort of output, you'll need to explain how the actual output differs from the desired output.

I took the liberty of fixing the indentation in the code -- this really helps for making the code readable, and a good editor should make it easy to use proper indentation (e.g. emacs, vi, ...)

I also did some refactoring, to remove unnecessary variables, make the output more informative, and use loops where possible.

I couldn't tell what you were trying to do with your "$seq" variable... that (and the output format) is the only place where my version does something different from yours -- but I'm just guessing about what you really want.

Read more... (7 kB)