[Bioperl-l] problem to fit genomic coordinates

[Sean Davis]

On Thu, Mar 26, 2009 at 11:30 AM, Laurent MANCHON
<lmanchon at univ-montp2.fr>wrote:

> okay, you are right,
> but i think in my opinion that my question is a good question about parsing
> enormous
> range of intervals.
> The problem is not perl, bioperl, or other language, it's just an
> algorithmic question.
> I'm not a professionnal in Bioperl and i don't know what is possible to do
> with all the Bioperl modules.
> So if you think it's possible to resolve my question with Bioperl maybe you
> are right, but in my position i stay in the same point.
> If you want i send you the two files needed in my question. And if you are
> agree try to use Bioperl to resolve it. Maybe it's not possible because
> files are big, i don't know.
>

To answer the question a bit more directly, you might consider using an
R-tree indexing scheme or something akin to the binning scheme that UCSC
uses for range queries.  Algorithms like those allow very fast range
operations.  If you want a sense of how fast, try using the galaxy server at
Penn State.

Sean


>
>
>
> Chris Fields a écrit :
>
>> (edited for those with sensitive eyes)
>>
>> Laurent,
>>
>> Please keep all responses, no matter how puerile, on the mail list ;>
>>
>> We're trying to point out the blatantly obvious: this isn't the place for
>> your question.  Sorry if that irritates you.  And, to reiterate, don't be
>> surprised if you get some nasty responses.
>>
>> chris
>>
>> (hoping this isn't one of the GSoC students, as he's introducing Laurent
>> to his spam filter)
>>
>> On Mar 26, 2009, at 10:04 AM, Laurent MANCHON wrote:
>>
>>  p*** off
>>>
>>> Chris Fields a écrit :
>>>
>>>>
>>>> On Mar 26, 2009, at 8:36 AM, Laurent MANCHON wrote:
>>>>
>>>>  Chris Fields a écrit :
>>>>>
>>>>>>
>>>>>> On Mar 26, 2009, at 3:31 AM, Laurent MANCHON wrote:
>>>>>>
>>>>>>  yes but this is a school problem that my teacher ask us to resolve
>>>>>>> without using Bioperl modules !
>>>>>>>
>>>>>>
>>>>>> I didn't bother reading beyond that sentence.  Not to state the
>>>>>> absolute obvious here, but:
>>>>>>
>>>>>> 1) you are posting to the bioperl list for a non-bioperl-related
>>>>>> question, and
>>>>>>
>>>>> genomic coordinates are not questions about biology ?
>>>>> i'm speaking about GENOME, and not GEOGRAPHY
>>>>>
>>>>
>>>> And this is a mail list for BioPerl (the toolkit), not perl and biology.
>>>>  We will sometimes answer questions along these lines if they are relevant,
>>>> but apparently our answers (all notably BioPerl-related, mind you) were
>>>> tossed to the side and you asked for more.
>>>>
>>>> I suppose you at least showed some honesty and revealed exactly why you
>>>> needed this answered, but again, don't be surprised if you get a nasty
>>>> response and no answers.  You won't get any from me.
>>>>
>>>>  2) you are committing one of the biggest no-no's for a list, asking us
>>>>>> to help you with your homework.
>>>>>>
>>>>> in bioperl you have BIO, okay but too you have PERL !
>>>>>
>>>>
>>>> Interesting how you skirted that last question.  We won't do your
>>>> homework for you.  Sorry.
>>>>
>>>> chris
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
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