[Bioperl-l] About FASTQ parser

[Chris Fields]

Abhi,

The FASTQ parser hasn't been released to CPAN yet.  It is available  
via bioperl-live.  We haven't added any code yet to the HOWTO's, but  
the SYNOPSIS example in Bio::SeqIO::fastq should be sufficient to get  
you started.

Bio::Seq::Quality is the object returned via next_seq(); it can be  
queried for PHRED qual scores and other bits.  If you want to split  
things up you should call next_seq(), then generate a FASTQ output  
stream in the variant you want:

my $outfasta = Bio::SeqIO->new(-format => 'fastq-sanger', -file =>  
'>fasta.file');
my $outqual = Bio::SeqIO->new(-format => 'fastq-sanger', -file =>  
'>qual.file');

while (my $seq = $in->next_seq) {
    $outfasta->write_fasta($seq);
    $outqual->write_qual($seq);
}

Note I haven't tested that yet, but it should work.  Let me know if it  
doesn't.

chris

On Sep 16, 2009, at 3:13 PM, Abhishek Pratap wrote:

> Hi Chris
>
> I remember seeing a recent email about new bioperl fastq parser. Is it
> part of bioperl 1.6 dist. I installed one and based on the doc
> here(http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqIO/fastq.html 
> )
> I am a bit lost.
>
> I see two methods there : using Bio::SeqIO::fastq and
> Bio::Seq::Quality. Are both same in terms of data returned and latter
> giving a scale up in speed ?
>
> This is not to offend any developer but small example/s on the HOWTO's
> helps a lot.
>
> The current example (copied below) is not working. I guess it is based
> on a previous version of code.
>
> # grabs the FASTQ parser, specifies the Illumina variant
> my $in = Bio::SeqIO->new(-format    => 'fastq-illumina',
>                          -file      => 'mydata.fq');
>
>
> My basic requirement is to read each read in fastq record and split it
> into header: read: quality.
>
>
> Thanks,
> -Abhi
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