[BioPython] [PopGen] a random Haplotype Sets generator

[Giovanni Marco Dall'Olio]

On Thu, Nov 13, 2008 at 11:34 AM, Tiago Antão <tiagoantao at gmail.com> wrote:
> I love the comment documentation, makes everything very easy to
> understand at first read.

It's doctest

> Where would you think this would fit in a PopGen hierarchy? Or to put
> it in another way, please complete Bio.PopGen....

Maybe we could create a module called 'Generators' where to put all
similar Generators.

p.s. are you using some kind of repository/rcs for you PopGen modules?
I just don't want to write code that will be difficult to reimplement
in the future PopGen module..

> Tiago
>
> On Thu, Nov 13, 2008 at 9:37 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
>> I am writing a module to generate semi-random sets of haplotypes.
>> For example, let's say you want a set of 100 sequences of 200 SNPs, in
>> which an hotspot is located in a certain position: the module is meant
>> to generate such datasets, mainly for testing purposes.
>>
>> You can find the code here:
>> - http://github.com/dalloliogm/biopython---popgen/tree/master/src/PopGen/Gio/HaplotypesGenerator.py
>>
>> Could you give me some suggestions about this? For example, which
>> kinds of haplotype model would you think it could be useful to
>> implement (see the function paramsGenerator)?
>> What do you think about the way I have written this code? Would you
>> implement it in a different way?
>>
>> --
>> -----------------------------------------------------------
>>
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>
>
>
> --
> "Data always beats theories. 'Look at data three times and then come
> to a conclusion,' versus 'coming to a conclusion and searching for
> some data.' The former will win every time."
> —Matthew Simmons,
> http://www.tiago.org
>



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My Blog on Bioinformatics (italian): http://bioinfoblog.it