[Bioperl-l] SeqAnal.pm, Prediction parsers

[hilmar.lapp@pharma.Novartis.com]

>
> So, I'm not sure how to go best. Should I create a separate base module,
> or merge it right away with SeqAnal.pm? The latter won't be without some
> consequences for the Blast parser, because it relies on it (I guess), and
> to be honest I don't really want to mess with this monster, I'm sure I'd
> break something.
>
> Any comments, suggestions? Steve? Ewan?

I have to admit, I'm all for making a new "analysis" base class, but if we
do this we should try to share it among the existing analysis classes, in
particular BPLite and HMMER.

     Okay. I hope Steve won't mind that I'm going to steal a couple of
     lines from SeqAnal.pm.
     So, the issues are: (could the authors of BPLite [Lorentz?] and HMMER
     (?) comment?)
     1) What functionality (properties, methods) would you like to see
     delegated to a generic base class, apart from program(), version(),
     date()?
     2) Do you already use a method parse()? There is then likely a name
     clash.

          Hilmar