[Bioperl-l] SeqAnal.pm, Prediction parsers

[Ewan Birney]

On Wed, 6 Sep 2000 hilmar.lapp@pharma.Novartis.com wrote:

> 
> 
> 
> 
> >
> > 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?)

HMMER is me I guess. <sigh>.

>      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.

Nope. Do we have to implement parse?

> 
>           Hilmar
> 
> 
> 
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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