[Bioperl-l] Bio::Seq::SeqWithQuality and Bio::SeqIO::phd

Chad Matsalla chad@sausage.usask.ca
Fri, 10 Aug 2001 17:31:45 -0600 (CST)

Hi all,

I have completed Bio::Seq::QualI, Bio::Seq::PrimaryQual, and

Bio::Seq::SeqWithQuality ISA qw(Bio::Seq::QualI Bio::PrimarySeqI) and can
be constructed a number of ways all of which result in a SeqWithQuality
object containing a PrimarySeq object, a PrimaryQual object, and bundles
of methods for attempting to set descriptors like id,  desc, etc for
the SeqWithQuality object where they are common between PrimarySeq
and Seq::Qual.

Complete POD and tests are in place.

Methods to set things like quality and sequence for the subobjects are set
up and work as I have forseen them.

I haven't CVS commit'ed them yet because I haven't received the permission
(should come RSN) but I would really like somebody who cares to take a
look at them. I put the modules I created in a little devel directory and
the t/ things use my modules from devel/blib and the rest of the Bioperl
modules from @INC. Any volunteers?

At them moment I am working on Bio::SeqIO::phd and I was going to design
such that it returns a SeqWithQuality object. Any opinions?

My thought for Bio::SeqIO::qual is that it should return a Bio::Seq::Qual
object and the user can create their own SeqWithQuality object if/when
they get the sequence. Any opinions on that?

Chad Matsalla