[Bioperl-pipeline] some transformer stuff

[Shawn Hoon]

> > 	my head is cloudy with jet lag but I had playing around with 
> > transformers
> > on the plane and had some small proposals. I am doing some multiple 
> > alignments
> > for phylogenetic tree building.
> 
> I wonder if Shawn ever takes a break ;)

Couldn't sleep and I couldn't resist playing with the powerbook :)


> This is excellent, as we get more and more people out there saying 
> "Iterators are cool" while in BioPipe we can't stand them... I am sure 
> we will end up reusing it quite often. I think it will also be 
> applicable to event-driven parsers by iterating over an event.

yup thats the idea. Cuz essentially in terms of performance for event parsing,
its the same whether you iterate in the transformer or at the start of
the IOHandler fetch. You are still iterating the same number of times.
This just accomodates more interfaces.

> Seems like a very sensible idea. Again, it will probably help for all 
> file-based pipelines. For example, if you want to extend the file-based 
> blast pipeline by adding a downstream analysis or transformer you'd 
> have to specify the dir and run through the files. Also one could 
> actually just use the file_dir to let the next module figure out what 
> it has to do (i.e. list files in directory and do what you are meant to 
> do with them). Thumbs up :)

Great, will go ahead with that.

> I am hopefully emerging from tons of annoying burocracy and will be 
> playing with biopipe, biosql, promoter analysis,etc. a lot more from 
> when I move to TLL.... now writing in a cab off to SIR to get a new EP 
> hopefully....

cool..good luck with the EP ;)


shawn

> 
> Elia
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************