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";

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In reply to Re^2: Faster and more efficient way to read a file vertically by Anonymous Monk
in thread Faster and more efficient way to read a file vertically by Anonymous Monk

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