ASCII conversion from bam file

Question

[Korsocius]

Dear all,

can you help me with one thing, I would like to convert ASCII quality to decimal Quality for each read and for each base in the read and write it into one row. Input bam file. Output rows, where will be phred Quality score (I am using Torrent technology, then -33).

I create one code, but it is only for all bam file to get Quality score, could you help me with this?

#! /usr/bin/perl

open (IN,"samtools view bezdup.bam |") ;

$vysledek=0;
$celkovy_pocet=0;
while (<IN>) {
    my @ascii = split '\t', $_;
    $jeden= $ascii[10];
    my @jedenacty= split //,$jeden;
    foreach $vypocet (@jedenacty) {
        $pomocna = ord($vypocet)-33;
        if ($pomocna >= 20)  {
            $vysledek++;
            #print "$pomocna\n";
        }
        $celkovy_pocet++;
    }
}

close (IN);
$quality= ($vysledek / $celkovy_pocet)*100;
print "$vysledek\n";
print "$celkovy_pocet\n";
print "$quality";

[Devon Ryan]

Do you want to write the decimal values as rows in a file or as rows of what? You appear to be computing them correctly in pomocna, so it's just a matter of processing it in an appropriate way for your goals.

Anyway, I assume you want a line printed for each read, so just iterate over pomocna before hitting the end of the while loop.

[Korsocius]

For eaxmple. If your read bam file there is in $11 ASCII code.

INPUT : bam file $11 column

OUTPUT: Decimal values for each base

input : <<<===98 output: 60 60 60 61 61 61 57 56

and same results for all rows in bam file (for all reads)

[Devon Ryan]

Right, so just iterate over pomocna before hitting the end of the while loop.

[Korsocius]

Thank you, I will try it, because perl is really new language for me...