[Bioperl-l] alignment and assembly

[Robson Francisco de Souza]

	Hi!

On Wed, 6 Mar 2002, Nancy Hansen wrote:
> I only recently saw last month's messages
> on alignments/assembly because I just joined
> the list, but this is exactly the kind of 
> thing I was thinking of working on.  Maybe
> a "Contig" class that inherits from 
> SimpleAlign, and a "Read" class inheriting
> from Seq?

	I'm (slowly) working on this right now and I've been talking to
Chad Matsalla lately. He wrote the sequence quality objects
(Bio::Seq::PrimaryQual and Bio::Seq::SeqWithQuality) and the quality
interface (Bio::Seq::QuaI) for bioperl (nice code :).
	I'm adding Bio::SeqFeature functionality (the same found in
Bio::Seq) to Bio::Seq::SeqWithQuality. I think that is necessary to
have a standard way to access the huge amount of information that is
associated with a sequence when it is part of an assembly (good quality
regions, secondary scores, etc.).
	I still haven't looked at Bio::SimpleAlign to see how to implement 
a Contig class from it (I remember Jason Stajich suggested this on a
previous message), but I hope to start working with that till next week.

> Before I caught on to object orientation, I
> coded up all kinds of perl routines for
> parsing ace files, and I still need them, but
> would like to develop them into something
> bioperl compliant.

	I did that too. :)
	Take a look at Chad's Consed.pm
(Bio::Tools::Alignment::Consed.pm). I'll try to adapt this class to some
of my needs (retriving Bio::Seq::SeqWithQuality objects from ace files,
etc - Chad, I'm almost there :).

> I'm still a Bio::Perl
> newbie, so any advice would be much
> appreciated!
> 	--Nancy

	See the bptutorial to understand how to use bioperl and then go to 
biodesign.pod in the bioperl distribution. This document is like a "why we
did it this way".
	Hope that helps,
				Robson