[Bioperl-l] Parsing fuzzy locations

Matthew Pocock mrp@sanger.ac.uk
Fri, 15 Dec 2000 14:56:56 +0000

> I did look at writing the parser in pure Perl, using "Parse::RecDescent" (see
> D.Conway, "The man(1) of descent", The Perl Journal, 12:46-58, winter 1998).  I
> suspect the grammer I developed (modified from the Genbank B-N form) would
> almost work for Parse::RecDescent, but some of the recursions might need to be
> re-ordered.  I went the flex/bison route as we have other programers who wanted
> a parser that could be accessed via C and C++.

RecDescent was what I used back in the mists of time, prety much directly from the
genbank B-N. It works fine. You have to think about how to represent the fuzzyness
in your location object-model (BioJava just decorates another location object adding
boolean properties fuzzyMin and fuzzyMax). As for complement & join, I think these
should in the simple case be propogated up as properties of the feature, but your
milage may vary.

Good luck.