My failed attempt: 

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" ;

         }
  }

}

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In reply to Re^2: how to process very large tab limited pileup file by gudluck
in thread how to process very large tab limited pileup file by gudluck

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