[Bioperl-l] Parsing PAML mlc files

Jason Stajich jason.stajich at gmail.com
Thu Sep 1 16:23:47 EDT 2011


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
> 
> 
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