[Bioperl-l] primer3, SeqIO::primer3, PrimedSeq, and SeqFeature::Primer

[Chad Matsalla]

On Fri, 9 Aug 2002, Ewan Birney wrote:
> My only concern Chad is whether the primer3 parser should be a SeqIO case
> - is this really the best model...

What do you feel are the guidelines for placing things in SeqIO? In my
opinion, the input belongs there because it takes a file and returns
sequences.

The writing and running is different. How do you think this should be
done?

> I have never run Primer3 (now... that tells you something...) --- what is
> in the output.

I placed sample input and output files in
t/data/primer3_(input|output).txt. Basically they are a two fields per
line, equals delimited, with an "=" alone on a line to delimit records.

> If Primer3 basically makes sequences features I would claim that a model
> closer to Bio::Tools::GFF is better than Bio::SeqIO

This could be. I will monkey around with things today and see how they
pan out.

Chad Matsalla


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