[Bioperl-l] Re: Assembly package and phredPhrap tools

[Chad Matsalla]

On Mon, 5 Nov 2001, Robson Francisco de Souza wrote:

> 	I have been working on a perl module to load information from
> phrap .ace files, phd files and some other things in the universe of
> phredPhrap's data. Although I haven't code it following bioperl's
> programming model, neither used bioperl's objects in its implementation, I
> would like to move my module to bioperl's approach. I was actually
> thinking of merging my code with Chad's code, but I believe that is gonna
> be hard so I would like to hear something from you (all of you
> and specially Chad) first.

Hi all,

I committed Bio::Tools::Alignment::Consed and Bio::Tools::Alignment::Trim
as well as some support files for testing and things.

These were originally written for a pipeline for a dual-pass
EST-sequencing pipeline and you can see that reflected in most of what it
does. I think, however, it might be of use to anybody doing clustering
using phrap, cap3, or cap4.

Bio::Tools::Alignment::Consed was created long before I wrote
PrimaryQual.pm and SeqWithQuality.pm so next time I have to work with this
code I will completely rewrite it. If people are using it I would, of
course appreciate improvements. (Robson? <hint><hint>)

The first set of rewrites will be the inclusion of proper bioperl IO
mechanisms. The second set of rewrites will have Consed.pm use PrimarySeq,
PrimaryQual, and SeqWithQuality objects. I wrote PrimaryQual and
SeqWithQuality after Consed.pm so you see the problem inherent in the
system.

Bio::Tools::Alignment::Trim is an ugly implementation
of a sliding-window-look-forward-average smoothing algorithm. Existing
programs didn't do the trick for us so I kludged that thing together.

This was created because existing trimming programs didn't do _exactly_
what we needed. This was tweaked into producing trimpoints that mimicked
the

I wouldn't really advise that people use this much. It operates, in my
context, as a part of Consed.pm and works well but it is a bit...
special. :)

Chad Matsalla