[Bioperl-pipeline] some transformer stuff

[Jer-Ming Chia]

Yes, go for it. I can definitely see the need for the iterator transformers.
Out of curiosity though, what's the method call for the IOHandler in the
case of an AlignIO?



> So the Iterator module basically takes in a IO-type object, figures out
whether its SeqIO
> or AlignIO etc and basically returns the array of objects. Not the most
efficient but
> it works for small number of inputs per file.
>
> So that works. The issue is whether we want to store full file paths in
the input table
> for each input name, which is messy if you are copying file inputs and you
want to figure out
> the base file name. Alternatively, what I think might be better is to add
a column file_dir in the stream
> adaptor table. So if its present, and the inputs are files, it will
concatenate it.
> The current way of handling files is at the analysis level where we assume
that files
> are simply passed to the analysis and the file_dir is an analysis
parameter. However for
> this case here, we need to put the file into objects and for the
transforming.
> in anycase, interested to hear your views.
>
> cheers,
>
> shawn
>
>
>
>
>
> --
> ********************************
> * Shawn Hoon
> * http://www.fugu-sg.org/~shawnh
> ********************************
>
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