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

[Ewan Birney]

On Mon, 31 Mar 2003, Rob Edwards wrote:

> Hi all,
>
> I have split Primer3 into Bio::Tools::Primer3 to parse Primer3 output and
> Bio::Tools::Run::Primer3 to run primer3, including adding the in OK_FIELD and
> AUTOLOAD methods as suggested by others.

great.

>
> Is there a way in Bio::Tools::Run::WrapperBase or Bio::Root::IO (or
> elsewhere?) to deal with creating a filehandle to print results out to? I
> couldn't find either a method or another implementation that has done this.
>

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?

> Also, I added a Bio::Tools::ePCR module that will return a Bio::Seq object
> when given a template and two sequences to act as primers. (I am not sure
> about the name at the moment, and am happy to change it as NCBI has an ePCR
> program that doesn't do anything like this).
>

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

> http://www.salmonella.org/bioperl/primer3_v0.2.tgz
>
> I'd appreciate any feedback.
>

we'll put this into bioperl once this discussion has rounded out...



> Rob
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