[Bioperl-pipeline] some transformer stuff

[Shawn Hoon]

On Thu, 27 Feb 2003, Jer-Ming Chia wrote:

> 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 IOHandler will simply have a 
Bio::AlignIO->new(-file=>"FILE_DIR/INPUTNAME",-format=>"msf");

then this object is passed to the transformer to iterate thru it.

shawn


> 
> 
> 
> > 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
> > ********************************
> >
> > _______________________________________________
> > bioperl-pipeline mailing list
> > bioperl-pipeline at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-pipeline
> 

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