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" ;
}
}
}