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

[K. Shameer]

Hi Jason,

Thanks for this information. I will go through this.

In case if somebody land this page from google using similar queries :
Please note that as I wanted this analysis to be completed asap, I
extracted genes in the chromosome regions using BioMart and used
List::Compare based methods to get the desired results.

Thanks,
Shameer

> You can use the collapse_nums method in Bio::Search::BlastUtils which is
> just an implementation of the connectivity algorithm but the Range
> description that Roy points out may be more useful since you'd have to
> unroll the ranges into the full set of numbers.
>
> collapse_nums
>
>   Usage     : @cnums = collapse_nums( @numbers );
>   Purpose   : Collapses a list of numbers into a set of ranges of
> consecutive terms:
>             : Useful for condensing long lists of consecutive numbers.
>             :  EXPANDED:
>             :     1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32
>             :  COLLAPSED:
>             :     1-6 10 12-15 17 18 20-22 24 26 30-32
>   Argument  : List of numbers sorted numerically.
>   Returns   : List of numbers mixed with ranges of numbers (see above).
>   Throws    : n/a
>
> -jason
> K. Shameer wrote:
>> 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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>>
>>
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