[Bioperl-l] TFBS databases, Bio::Matrix::PSM suitable?

Sendu Bala bix at sendu.me.uk
Tue Aug 22 13:00:27 EDT 2006


skirov wrote:
>>>> Stefan Kirov wrote:
>>>> Sendu Bala wrote:
>
>> I'm not sure what you mean. Do you think that before a genbank parser
>> can be released, all genbank files in existence must be supplied in the
>> test suite to ensure it really does work on everyone's machine? 
 >
> Did I say that or you infer? What I said is the tests are prepared to make 
> sure the code work properly under specific environment (architecture, 
> compiler, etc.) However, developers must make sure their code does not get 
> choked up by the full data set.

I would have thought this went without saying. Of course the original 
developer checks to see if his code works on the full data. The question 
is does every user of bioperl need to be able to test the full data? No. 
Until recently, Bio::DB::Taxonomy::flatfile wasn't tested at all. I 
didn't see you complain at my suggestion a subset of the taxonomy 
database be included in t/data for testing purposes.


> My point exactly- how bioperl contributors can fix a bug if they do not have 
> access to the data? It means the user would have to submit a test set which 
> could be a license violation. I do not know to what extent Transfac would 
> pursue their rights and its implication, but I wouldn't like to try either.

Look, the TFBS:: module seems to have survived without causing anguish 
and heartache. If /you/ don't have access to the data maybe you can't 
fix some possible future bug. But the nice thing about an open-source 
project like Bioperl is that maybe someone else /does/ have access, and 
/they/ can fix the bug.


>> Who says it won't be maintained? I will maintain it. The very second I
>> can no longer maintain it and no one else can, it can be deprecated to
>> avoid clutter. I don't see the problem. But in any case see below -
>> anyone could probably maintain it.
 >
> I guess that if you decide you can no longer do that you are going to remove 
> it? Go ahead, but do not forget what you are promising now.

I made no such promise. It is the case that with all modules in bioperl 
that if they are no longer maintained and no longer work, they should be 
deprecated. My proposed module would be different in this regard.


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