[Bioperl-pipeline] Re: Genewise...

[Elia Stupka]

> Hmmm... i'm not exactly sure what u mean here .. do u suggest that we create
> another Bio::Tools::Genewise module that contains the parsing code and run
> it from Bio::Tools::Run::Genewise ? I can't find an example of this...

Sorry I just realised I miswrote one thing, the Bio::Tool::program is in
bioperl-live, and the Bio::Tools::Run::program is in bioperl-run

Most of them are like this, see:

Bio::Tools::Eponine (and Bio::Tools::Run::Eponine)
Bio::Tools::Genscan (and Bio::Tools::Run::Genscan)

So Pseudowise,Genewise,RepeatMasker all need to be fixed that way...

(sorry I hadn't noticed earlier)

Elia



> >
> > We should also make sure that the parsing is robust (no I didn't get
> > around it, yes, I do overestimate time I have left for coding sigh sob
> > sigh)
> 
> OK... i will implement a matching operator to sieve out the score instead of
> assigning it to an arbitrary element..
> 

Elia

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