[Bioperl-l] Bio::Coordinate mappers

[Heikki Lehvaslaiho]

Arnaud Kerhornou from Sanger has confirmed that my latest fixes to the
Bio::Coordinate::GeneMapper really work. The fixes are now only in the
CVS head but will be ported to the 1.2 branch before the upcoming bug
fix release.

Feel free to start using the modules now. 

There are general purpose coordinate mapper objects (Pair, Extrapolating
Pair, Collection, Chain) which have been used to build a gene-centred
mapper: GeneMapper. A GeneMapper models one transcript which has CDS
start and end, and one ore more exons. When the object is primed with
these values,  generates all the internal mappers. The user can select
the used input coordinate system and desired output coordinate system
and pipe sequence locations through. The built-in coordinate systems are
identified by (hopefully) self-explanatory  names: peptide, propeptide,
frame, cds, negative_intron, intron, exon, inex, gene, chr.

An overview of classes is is given in models/coordinatemapper.dia file.

	-Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________