[Bioperl-l] PAML

Chris Fields cjfields at uiuc.edu
Sun Oct 29 09:23:45 EST 2006


Does the data show up in the object using Data::Dumper?

This should be filed as a bug since the docs imply the method  
exists.  This could be written up fairly quickly if one had test data  
and and a script to work with (hint hint...)

Chris

On Oct 29, 2006, at 4:52 AM, Albert Vilella wrote:

> I don't know if this method is implemented. I can't grep-find it.
> Maybe it's simply not there yet, but was planned when the
> documentation was written.
>
> On 10/28/06, Eric Ross <eric.ross at neuro.utah.edu> wrote:
>> I am trying to extract the "Naive Empirical Bayes (NEB)  
>> probabilities" from a Bio::Tools::Phylo::PAML::Result object.
>>
>> I am able to extract other data from the report, but there seems  
>> to be a conflict in the documentation.  One doc implies that there  
>> should be a get_posteriors method. (It's used as an example in the  
>> Bio::Tools::Phylo::PAML doc), but the method does not appear to  
>> exist in the Bio::Tools::Phylo::PAML::Result object.
>>
>>
>> I have been trying various methods, in the event I'm just  
>> "confused", but I've had no luck, thus far.  Anyone have suggestions?
>>
>>
>> code:
>>
>> ----begin code-------
>> #!/usr/bin/perl -w
>>
>> use strict;
>>
>>
>> use Bio::Tools::Phylo::PAML;
>> my $parser = new Bio::Tools::Phylo::PAML
>>              (-file => "mlc");
>> my $result = $parser->next_result;
>> my @posteriors = $result->get_posteriors();
>>
>> print "@posteriors";
>>
>> exit(0);
>>
>> ---------end code-------------
>>
>>
>>
>> ---------------
>> Eric Ross
>> Computer Analyst II
>> ejr at neuro.utah.edu
>> Howard Hughes Medical Institute
>> University of Utah
>> Sánchez Lab
>>
>>
>>
>>
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>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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