[Bioperl-l] Coordinate mapping

[David Block]

Genquire does this as well - I had a lot of fun creating a coordinate system ad-hoc while maintaining bioperl semantics.

Good luck with the off-by-ones!
You can look in Genquire: GQ::Server::GenericFeature.pm - 
That's where my transformations were.

--
David Block                    dblock@gnf.org
GNF - San Diego, CA        http://www.gnf.org     
Genome Informatics  /  Enterprise Programming

> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk]
> Sent: Thursday, June 20, 2002 7:04 AM
> To: Ewan Birney
> Cc: Bioperl
> Subject: Re: [Bioperl-l] Coordinate mapping
> 
> 
> 
> I'll do it - once I understand the code...
> 
> 	-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
___ _/_/_/_/_/________________________________________________________

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