[Bioperl-l] Fasta Qual files

Brian A. Desany, Ph.D. bdesany@bcm.tmc.edu
Thu, 14 Sep 2000 11:44:11 -0500

The thing that comes to my mind is that since you can't have qual values
without a sequence, quality vals could be just another attribute on a
regular sequence object, but with its own (possibly complicated) mechanism
for being set accurately. Is that what you are saying?

> Is there a means to deal with
> fasta.qual files
> > within bioperl (Bio::SeqIO::fastaqual, like), or does
> anyone have any other
> > suggestions as to how to handle this independently? Thanks,
> The way to handle this is to probably have the following set up
>   Bio::PrimarySeqWithQualityScores - object representing the
> sequence with
> quality scores. This should at least implement the Bio::PrimarySeqI
> interface and possibly inheriet from Bio::PrimarySeq for its
> implementation
>   Bio::SeqIO::quality - seqio system to read
> PrimarySeqWithQualityScores
> Of course the problem is that the quality scores and sequecne actually
> come in different files (though usually named the same). So -
> this is not
> a perfect fit. A second object might come into play.
> does this give you some ideas?