[Bioperl-l] Bio::SeqFeatureProducer

[Jason Stajich]

(Hilmar, if you can help be my verifier that we have completed all the
parts of the task, we can start to tick off some of the things from the
tasklist...)

I commited a new class Bio::SeqFeatureProducer, a test file, and more test
data.  

One can use this class to simplify the way Features from an analysis are
added to a sequence (Genes from Bio::Tools::Genscan or Bio::Tools::MZEF).  

In some cases you will want more fine grained control over how features 
are added or seen so that more information is produced in a Genbank/EMBL
dump.  This can be done by cycling through the features on the sequence
and processing them.  ie I want to dump CDS and predicted protein
translation in genbank files from genscan analysis, I have to take each
gene on the seq, add a new feature for CDS with a translated field.
Perhaps we can work out a way for the GeneStruct objects to be dumped a
little more informatively?

I suspect we will want to remove Bio::SeqFeatureProducerI as I don't
think it is necessary unless we will have many different ways to
add_features to sequences with non AnalysisParserI objects...  

Anyone else writing parsers - GAME w/o seq and gff will certianly fit here
with a simple wrapper - should make sure they have a class that implements
SeqAnalysisParserI and then SeqFeatureProducer can take advantage of the
class.  Will have to add them to the %DRIVERVALUES variable in
SeqFeatureProducer since we don't have parsers in a central location.

Hope this is useful.

-jason

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/