[maker-devel] Question about 'keep_pred' setting

[Carson Holt]

There is a hidden score called abAED that measures concordance among the ab
initio gene predictors .  The idea was to have ab initio models that are the
same across multiple ab initio predictor be kept if they're group
concordance is high enough, then drop ab initio predictions that only happen
in one ab initio predictor.  Currently the option is all or nothing, the
threshold would give a more fine grained control of keeping just some
unsupported predictions.

--Carson


From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Thursday, May 29, 2014 at 2:47 PM
To:  Daniel Ence <dence at genetics.utah.edu>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Question about 'keep_pred' setting

Thanks.

Just curious: how would the intended behavior differ if keep_pred was set
to, say, 0.5, instead of 0 or 1?


--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University


On Thu, May 29, 2014 at 4:44 PM, Daniel Ence <dence at genetics.utah.edu>
wrote:
> Hi Daniel, 
> 
> Your interpretation of the code is correct. keep_preds is a binary setting.
> There's been some discussion behind-the-scenes about making it more flexible,
> but that hasn't been implemented yet. We need to fix what it says in the
> control file. 
> 
> 
> Daniel Ence
> Graduate Student
> dence at genetics.utah.edu
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> On May 29, 2014, at 2:37 PM, Daniel Standage <daniel.standage at gmail.com>
>  wrote:
> 
>> Good afternoon!
>> 
>> I have a quick question about the keep_pred setting in Maker. In older
>> versions of Maker, this was a binary value indicating whether unsupported
>> predictions should be kept. I'm now using Maker 2.31.3, where it's described
>> as a scaled value indicating a "concordance threshold" for unsupported
>> predictions. As far as I can tell from the code, however, it's still treated
>> in the same way as before.
>> 
>> Could you briefly describe the motivation for this setting and the intended
>> (although possibly incomplete) change in its functionality in new versions of
>> Maker?
>> 
>> Thanks!
>> 
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Computational Genome Science Laboratory
>> Indiana University
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 

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