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

[K. Shameer]

Hello Roy,

Thanks for the pointers.

--
Shameer

> 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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