[Bioperl-l] PAML

Eric Ross eric.ross at neuro.utah.edu
Sat Oct 28 17:24:30 EDT 2006


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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