[maker-devel] Question about 'keep_pred' setting

[Daniel Standage]

Ah, that makes sense. Thanks!


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


On Thu, May 29, 2014 at 5:43 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
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>>
>>
>>
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