[Bioperl-l] Directions for qual modules.

[Heikki Lehvaslaiho]

Chad Matsalla wrote:
> I know about the different formats that phred can write but at the moment
> I really only care about phd files:
> BEGIN_DNA
> a 6 1
> c 6 20
> t 6 17
> ...
> and fasta-style files containing quality values only. These are what can
> be found in phrap'ed consed project directories.
> 
> <thinking>
> Should there be a Bio::SeqIO::phd and Bio::SeqIO::xbap and so on, one for
> each type of file? This sounds good to me and doesn't break the fact that
> at this time my Bio::SeqIO::qual only parses fasta-style quality files. It
> also seems more intuitive to do things this way rather then to pass in
> some flag when then SeqIO object is constructed.
> 
> my $in_qual  = Bio::SeqIO->new(-file => "<t/qualfile.qual" , '-format' =>
> 'qual');
> my $in_qual  = Bio::SeqIO->new(-file => "<t/phredfile.phd" , '-format' =>
> 'phd');
> my $in_qual  = Bio::SeqIO->new(-file => "<t/quality.xbap" , '-format' =>
> 'xbap');
> 
> Heikki, how does this tie into your idea of a Bio::Seq::QualIO? How would
> this account for .phd files with both quality and sequence?
> Bio::Seq::QualIO might only be intuitively useful for files (like my
> fasta-quality files) with quality values only. I am really interested in
> phd files (like above) that have both quality and sequence.

I did not realise that the the sequence and quality are in the same
file.
This just shows how long time it is I did any sequencing. ;-)

The above code example is fine. Go for it.

	-heikki
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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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