eric.ross at neuro.utah.edu
Sun Oct 29 12:06:54 EST 2006
Thanks for all the help.
I've been looking at the code for the PAML rst parser. It's a bit tricky.
We have written a parser specific for our needs, but it looks to be a pretty complicated matter to make it generic.
The output of PAML can vary a lot depending upon your options and this section can be repeated multiple times. I'm sure someone with a good grasp of the potential output of PAML could come up with something, but I'll admit to being at a loss.
Computer Analyst II
ejr at neuro.utah.edu
Howard Hughes Medical Institute
University of Utah
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Sun 2006-10-29 7:23 AM
To: Albert Vilella
Cc: Eric Ross; Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] PAML
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...)
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?
>> ----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";
>> ---------end code-------------
>> Eric Ross
>> Computer Analyst II
>> ejr at neuro.utah.edu
>> Howard Hughes Medical Institute
>> University of Utah
>> Sánchez Lab
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Bioperl-l mailing list
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