[Bioperl-l] How to print encoded fastq quality string?

[Smithies, Russell]

A bit hacky and there's probably a "proper" way to do it but this works:


while (my $seq = $in->next_dataset()) {
	print  %{$seq}->{'-id'},"\n";
	print  %{$seq}->{'-raw_quality'},"\n";
	print  %{$seq}->{'-seq'},"\n";
	print  join ' ',@{ %{$seq}->{'-qual'}},"\n";
}



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Peng Yu
> Sent: Tuesday, 8 June 2010 1:15 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] How to print encoded fastq quality string?
> (Bio::Seq::Quality)
> 
> Hello All,
> 
> I want to retrieve the original encoded quality string. But it seems
> that Bio::Seq::Quality has already converted them into numerical
> array. Is there a method that can help retrieve the original encoded
> quality string such as
> "ffffff`edfffeeff^ffefffeeeef`ffcf`deedaYcceecdcedaffffefaaYfc`ccc`TdaYT^L
> Tb"?
> 
> --
> Regards,
> Peng
> 
> $ cat main.fastq
> @HWI-EAS11X_10097:4:1:1909:9532#0/1
> CGCGGGGATGACTCTAAGCATGGTGCAGGCGATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCT
> C
> +
> ffffff`edfffeeff^ffefffeeeef`ffcf`deedaYcceecdcedaffffefaaYfc`ccc`TdaYT^LT
> b
> @HWI-EAS11X_10097:4:1:1948:6460#0/1
> CATGGCTTACATGCTGAGTGCCAACATGGACCAGGGAGATCGGAAGATCGGTTCAGCAGGAATGCCGAGACCGA
> T
> +
> dc^c^dddadLcccLc\^acaa^Yca^caYYcacc^YbJ^aTcaT`KKacY\LL\c^\YTTYLL\TL_T_BBBB
> B
> @HWI-EAS11X_10097:4:1:1986:2311#0/1
> CTAGGCTTCCTCCCCTCCGTCAGGGCCACTCTCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATA
> T
> +
> effaYefffcffdfecefbeffdce^eLedd`e\YcaceeffcYeaeee\ddcT\\TaYTaddbYbbL^Y]LZL
> ]
> $ cat main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> use Bio::SeqIO;
> 
> my $in=Bio::SeqIO->new(-file => "main.fastq", -format => 'fastq-
> illumina');
> 
> while (my $seq = $in->next_seq()) {
>   print ref($seq), "\n";
>   print $seq->qual_text, "\n";
> }
> $ ./main.pl
> Bio::Seq::Quality
> 38 38 38 38 38 38 32 37 36 38 38 38 37 37 38 38 30 38 38 37 38 38 38
> 37 37 37 37 38 32 38 38 35 38 32 36 37 37 36 33 25 35 35 37 37 35 36
> 35 37 36 33 38 38 38 38 37 38 33 33 25 38 35 32 35 35 35 32 20 36 33
> 25 20 30 12 20 34
> Bio::Seq::Quality
> 36 35 30 35 30 36 36 36 33 36 12 35 35 35 12 35 28 30 33 35 33 33 30
> 25 35 33 30 35 33 25 25 35 33 35 35 30 25 34 10 30 33 20 35 33 20 32
> 11 11 33 35 25 28 12 12 28 35 30 28 25 20 20 25 12 12 28 20 12 31 20
> 31 2 2 2 2 2
> Bio::Seq::Quality
> 37 38 38 33 25 37 38 38 38 35 38 38 36 38 37 35 37 38 34 37 38 38 36
> 35 37 30 37 12 37 36 36 32 37 28 25 35 33 35 37 37 38 38 35 25 37 33
> 37 37 37 28 36 36 35 20 28 28 20 33 25 20 33 36 36 34 25 34 34 12 30
> 25 29 12 26 12 29
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