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

Hilmar Lapp hilmarl@yahoo.com
Sat, 11 Aug 2001 12:56:32 +0200

Chad Matsalla wrote:
> Hi all,
> I have completed Bio::Seq::QualI, Bio::Seq::PrimaryQual, and
> Bio::Seq::SeqWithQuality.
> 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?

Chad, I think you can go ahead and cvs commit if tests pass on
your side. It is generally understood that there may be bugs and
missing documentation in the first place, that's not a problem at
all. Just commit then people can check it out (and run e.g. the
tests on their side).

> 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?

Sounds good as far as I'm up-to-date.

> 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?

Sounds OK.


Hilmar Lapp                              email: hilmarl@yahoo.com
A-1120 Vienna

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