So basically I have this (brute-force attack):
while(<>)
{
if($_=~/^(.*?)\t(.*)/)
{
$read_seq=$1;
$read_id=$2;
@split_read=split(//, $read_seq);
$respective_read_letter=$split_read[$i];
if($respective_read_letter eq 'A')
{$count_A++;}
elsif($respective_read_letter eq 'T')
{$count_T++;}
elsif($respective_read_letter eq 'C')
{$count_C++;}
elsif($respective_read_letter eq 'G')
{$count_G++;}
elsif($respective_read_letter eq '.')
{$count_dot++;}
else
{print "ERROR in read: $read\t$respective_read_letter\
+n";}
}
}
$total=$count_A+$count_T+$count_C+$count_G+$count_dot;
$fraction_A = sprintf("%.2f", 100*($count_A/$total));
$fraction_T = sprintf("%.2f", 100*($count_T/$total));
$fraction_C = sprintf("%.2f", 100*($count_C/$total));
$fraction_G = sprintf("%.2f", 100*($count_G/$total));
$fraction_dot = sprintf("%.2f", 100*($count_dot/$total));
print $actual_pos,"\t",$expected_letter,"\t",$fraction_A,"\t",$fra
+ction_T,"\t",$fraction_G,"\t",$fraction_C,"\t",$fraction_dot,"\n";