[Bioperl-l] Coordinate mapping

[Ewan Birney]

On Thu, 20 Jun 2002, Heikki Lehvaslaiho wrote:

> 
> I'll do it - once I understand the code...
> 

Arne and I both understand the code ;). The key point is that one has the
ability to map to disjoint regions, ie:


   @mapped_regions = $mapper->map('A',$start,$end,$strand)

where @mapped_regions is a list of id,start,end,strands *OR* gaps. The
gaps are crucial - this way you know if you are missing stuff off the
start or the end.


The other annoyance is that one set of functions handles both the forward
and the revese mappings and has weird symmetry things to address the
correct hashes.


> 	-heikki
> 
> 
> Ewan Birney wrote:
> > On Thu, 20 Jun 2002, Heikki Lehvaslaiho wrote:
> > 
> > 
> >>I am going to commit a first version of the  Bio::Coordinate::Mapper.pm 
> >>module today. I'll start writing it so that it converts integer value form 
> >>one coodinate system to an other and then later take into account 
> >>(subclassing or overwriting) Bio::Location start/end pairwise locations.
> >>The coordinate systems can have values like peptide, propeptide, cds, 
> >>transcript, gene, clone, ...
> > 
> > 
> > 
> > Heikki - before you start - why not import the Bio::EnsEMBL::Mapper::*
> > wholesale into Bioperl (though it wont do 1 ---> 3 mappings, ie DNA --->
> > protein). 
> > 
> > Hmmmm.
> > 
> > 
> > 
> >>I will be committing quite often. This is the second time I am starting to 
> >>write this module. I lost the first version when my laptop crashed :-(
> >>
> >>	-Heikki
> >>
> >>-- 
> >>______ _/      _/_____________________________________________________
> >>       _/      _/                      http://www.ebi.ac.uk/mutations/
> >>      _/  _/  _/  Heikki Lehvaslaiho          heikki@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
> >>___ _/_/_/_/_/________________________________________________________
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l@bioperl.org
> >>http://bioperl.org/mailman/listinfo/bioperl-l
> >>
> > 
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
> 
> 
> -- 
> ______ _/      _/_____________________________________________________
>        _/      _/                      http://www.ebi.ac.uk/mutations/
>       _/  _/  _/  Heikki Lehvaslaiho          heikki@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
> ___ _/_/_/_/_/________________________________________________________
> 
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------