[Bioperl-l] Any module for chromosome region analysis ?
shameer at ncbs.res.in
Wed Feb 24 17:05:25 EST 2010
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.
> 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.
> 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
> K. Shameer wrote:
>> Hello Roy,
>> Thanks for the pointers.
>>> 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.
>>> 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
>>>> 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
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