[Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer

[Rob Edwards]

> usually this is something which is parsed into a datastructure and then an
> output stream from the features is built by the user. .... so I'm missing
> why you would need to open a write file "inside" the tool. Generally the
> user should be doing file opening etc. Can you flesh out the use case a
> little more?

Bio::Tools::Primer3 will parse into into a data stream so that you can get 
one result at a time. (It also has other output options too).

I needed to output the raw results so I could test that Bio::Tools::Primer3 
would parse a results file correctly :)

But also, this is from Heikki:
> * One should be able to quickly write one module to run an analysis and
> then  save the raw output in a named file and/or parse the output into
> objects (e.g. SeqFeatures).

I think it is a good idea to be able to easily save raw output from external 
programs so that if you change your mind later on about what results and/or 
format you want you only need to run the parser again and not the whole 
program. By having the raw output there is a better chance that next time 
around you will be able to correctly parse it.


> The name is *not* good ;) Would Bio::Tools::PCRSimulation be a good idea?

Yes. It would be a good idea.

Rob