[Bioperl-l] Parsing PAML mlc files

Dave Messina David.Messina at sbc.su.se
Fri Sep 2 05:30:33 EDT 2011


Looking back at the commit history, back in April and May 2010, I made some
updates for the January 2010 edition of PAML 4.4. All tests passed at that
time, but:

- the tests may be incomplete
- PAML has undoubtedly changed since then, even if it's still called version
4.4


I can't look at this right now myself, but please file a bug report on this,
and hopefully someone else can.


Dave




On Thu, Sep 1, 2011 at 22:23, Jason Stajich <jason.stajich at gmail.com> wrote:

> Lorenzo -
>
> I am sure this is a problem with changes in the output from PAML - this is
> classic problem with this suite.  This requires some debugging of the
> parser, not sure if there is anyone out there with time to do the debugging.
> I can say all this worked before on an earlier version of PAML but I don't
> know specifically what is going on with the latest paml4.4 version.
>
> Jason
>
>
> On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:
>
> > Hi all,
> > I'm trying to parse mlc output files from PAML using
> Bio::Tools::Phylo::PAML as:
> >
> > my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> > my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> > if ( my $paml_result = $parserF->next_result )
> > {
> > say Dumper $paml_result; #Prints Ok
> >       for ( my $model_result= $paml_result->get_NSSite_results )
> >       {
> >        #say Dumper $model_result; #Prints nothing
> >        $ns_string = "model ".$model_result->model_num."\n
> > ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> >       $dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> >       #say Dumper $dnds_site_classes;
> >       for my $sites ( $model_result->get_BEB_pos_selected_sites )
> >        ...
> >         ...
> >          ...
> >
> > The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> > DUmper. In contrast, it seems that the
> Bio::Tools::Phylo::PAML::ModelResult
> > object is not being properly instantiated, as I get the error message:
> >
> > "Can't call method "model_num" without a package or object reference at
> ..."
> >
> > What am I missing?
> > Best,
> > Lorenzo
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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