[Bioperl-pipeline] Biopipe Converters

[Shawn]

I'm taking a look at converters and pipeline.

I propose keeping converters within the pipeline.
Converters are mainly bridges between two objects that have evolved
separately from two projects, in this case, bioperl and ensembl.
I don't foresee any use case outside of biopipe. People will deal with
objects using only bioperl or using ensembl solely. It is only when
using biopipe that we will encounter the need for conversion. Rather
than trying to be too flexible now, I propose keeping the converter the
same as SeqFeatureIO just that we keep it within biopipe while still
using the Factory type pattern.

So we have a Converter.pm as we do now and  Bio::Pipeline::Converter::*
for the real converters. We just have to port the SeqFeatureIO code
over.

I expect  converters to be slightly hacky in the beginning and thus more
worthy to keep in "in-house" for now and not worry about making it too
generic for now. It also makes for better packaging right now, rather
than keeping it on the Fugu CVS or worrying about packaging it with
bioperl.These are standalones modules, people can still do a
Bio::Pipeline::Converter or Bio::Pipeline::Dumper without a pipeline. If
its more mature, we can move it to bioperl or something.


comments? 
before I launch into it.


shawn