[Bioperl-l] existing support for location w/ offset?

Sendu Bala bix at sendu.me.uk
Mon Oct 6 17:57:53 EDT 2008


George Hartzell wrote:
> I have a community that likes to refer to positions as offsets,
> e.g. 100 bases upstream of the beginning of the exon, or 5 bases after
> the splice site....  They think of it as 34532+2 or 23451-23 (funny,
> if you hold down the shift key when you type that, you get @#$%!-@#,
> which is how I feel about it...).
> 
> Are there any exising Bio::Location classes that would make keeping
> track of this info easier?

It might not be at all appropriate, and hopefully there's better 
solutions, but for relative positioning stuff you can try playing with 
Bio::Map stuff.


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