[Bioperl-l] SiteMatrix changes

Sendu Bala bix at sendu.me.uk
Thu Aug 31 15:42:04 EDT 2006


skirov wrote:
>
>> P0      A      C      G      T
>> 01      1      2      2      0
>> 02      2      1      2      0
>> 03      3      0      1      1
>> 04      0      5      0      0
>> 05      5      0      0      0
>> 06      0      0      4      1
>> 07      0      1      4      0
>> 08      0      0      0      5
>> 09      0      0      5      0
>> 10      0      1      2      2
>> 11      0      2      0      3
>> 12      1      0      3      1
[...]
>> If we revert all my changes the answer given is:
>>
>> NNNNNNNNNNNN
> I would say that this is the right answer in this case.

What's your reasoning there?

>> If you think you can fix this bug another way (that isn't specific to
>> Bio::Matrix::PSM::IO::transfac), I'll revert the changes and create a
>> bug report for you.
> Sounds OK with me. To summarize:
> 1. Correction is disabled by default.
> 2. Correction should be applied to all positions.
> 3. Thresholds for IUPAC consensus can be user defined.
> 4. A fix for IUPAC consensus calculation: change the defaukt behavior.
> 5. Document the options
> Does this sounds right?

Yes, sounds good to me. I'll code those up shortly. Aaron mentions some 
valid points, but I personally don't have the time or inclination to do 
any major changes.




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