[Bioperl-l] About FASTQ parser

[Abhishek Pratap]

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