[Bioperl-l] SeqAnal.pm, Prediction parsers

Ewan Birney birney@ebi.ac.uk
Wed, 6 Sep 2000 14:07:52 +0100 (GMT)

On Wed, 6 Sep 2000, Hilmar Lapp wrote:

> I'm finding myself duplicating some basic functionality across the
> prediction parsers GenScan, MZEF, and (under development) ESTScan.
> Creating a base class like PredictionParser (which also maps
> next_feature() to next_prediction() and could readily provide the
> SeqAnalysisParserI [watch out for Jason's coming announcement]
> implementation) seems to be intuitive.
> Now there is already SeqAnal.pm, which doesn't seem to used anywhere else
> than Blast.pm and its dependencies. Looking at the code, I find that
> 1) it is partially complete overkill for my purpose (i.e., half of the
> functionality is not only not needed but not applicable), 
> 2) some methods are not optimally designed, like length() (first, it
> forces you to put CORE::length() in every inheriting module, i.e., is a
> potential bugger, second, in those cases where it makes sense there are
> two sequences and not one for which you want the length, namely query and
> subject seq),
> 3) some functionality like program(), version(), date() is certainly
> useful in a basic PredictionParser, too,
> 4) parse() clashes with parse() in SeqAnalysisParserI
> 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. 

> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420