[Bioperl-l] SiteMatrix changes

skirov skirov at utk.edu
Fri Sep 1 13:14:09 UTC 2006

>===== Original Message From Sendu Bala <bix at sendu.me.uk> =====
>Sendu Bala wrote:
>> skirov wrote:
>>> 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.
>This is now done. I didn't quite do it the way you suggested: the
>'threshold' for IUPAC consensus is implemented as significance level for
>rounding the frequencies. This way we don't have to suffer some
>arbitrary cutoff that does unexpected things. You may also want to check
>the changes to the documentation (mostly in new() and the description)
>to make sure I understood and explained everything well enough.
Thanks Sendu. I will do that.

>The consensus string now also enforces the supplied or default
>threshold, and treats the threshold the way most people might think of
>such a thing - the minimum acceptable value (inclusive). This doesn't
>seem to actually change the answer for the few test matrices used by the
>test scripts (though the test script answers have changed since we're
>not doing pseudo-count correction anymore).
>One issue is that there's no way for the user to decide to do
>pseudo-count correction or not when using the PSM::IO modules. The
>correction should probably be farmed out to a separate method. I don't
>plan to do this myself.
I will look into this.
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