[Bioperl-l] What's the best object to store sequence assembly information?

[Heikki Lehvaslaiho]

David,

I've recently written modules to represent relationships between two
coordinate systems, e.g. clones vs contigs, but have not properly
announced them to the list. These objects should be fine for assemblies,
too. Have a look at the Bio::Coordinate namespace in the bioperl-live
CVS repository. Bio::Coordinate::Pair represents continuous match and
Bio::Coordinate::Collection is close to an assembly.

	-Heikki


On Thu, 2002-08-15 at 22:30, David Yerushalmi wrote:
> Hi,
> 
> I am working on an object that stores information from
> a Celera SNP XML file.  Each record contains data
> about a specific dna sequence that was used in an
> assembly during snp discovery.  Here's the information
> i need to encapsulate:
> 
> 1)  bioseq_id
> 
> 2)  assembly_begin
> 
> 3)  assembly_end
> 
> 4)  orientation
> 
> 5)  offset
> 
> The XML record looks like this:
> 
> {POLY_INSTANCE_ASSEMBLY}
> 
>               {BIOSEQ_ID}12345{/BIOSEQ_ID}
> 
>               {ASSEMBLY_BEGIN}617{/ASSEMBLY_BEGIN}
> 
>               {ASSEMBLY_END}617{/ASSEMBLY_END}
> 
>               {BIOSEQ_TYPE}2{/BIOSEQ_TYPE}
> 
>               {ORIENTATION}+{/ORIENTATION}
> 
>               {OFFSET}0{/OFFSET}
> 
>        {/POLY_INSTANCE_ASSEMBLY}
> 
> Do you have any suggestions on what existing bioperl
> class if any would be suitable to store this
> information? 
> 
> -david
> 
> 
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      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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