[Bioperl-l] PAML

Albert Vilella avilella at gmail.com
Sun Oct 29 05:52:04 EST 2006


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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