[Bioperl-l] Any module for chromosome region analysis ?

[Roy Chaudhuri]

Hi Shameer,

You could do this using Bio::Range, but that only allows you to 
determine the intersection between two ranges at once, so you'd need to 
do the calculation in several stages. It also doesn't have a method to 
determine positions that are unique to one of the ranges (although it 
possibly should).

As this isn't a problem that is specific to biology, it's also worth 
hunting around on CPAN for modules that may be useful. 
Set::IntSpan::Fast looks suitable, particularly the intersection and 
diff methods. I haven't tried it, though.

Roy.

On 24/02/2010 16:59, K. Shameer wrote:
> Hello all,
>
> I am looking for a standard way / bioperl module that can take up
> different chromosome regions (in basepairs) and give the unique and common
> regions.
> For example these are the regions and I need to get the common regions
> (start - end) among all 5 regions:
> 24328000 - 29166946
> 25388351 - 27114603
> 22310186 - 25239677
> 28511024 - 29638159
> 23729632 - 26385029
>
> Thanks,
> Shameer
>
>
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