[Bioperl-l] PAML parser

Jason Stajich jason at bioperl.org
Tue Jun 26 19:22:20 EDT 2007


Can you make sure you have the latest and greatest version of these  
modules from the CVS repository?  We had to fix things to parse 3.15  
-- I can't tell if this is the problem or something else.
You can also add -verbose => 1when you initialize the object and it  
may spit out more warnings about whether it is having problems.


-jason

On Jun 26, 2007, at 11:59 AM, Felix Schlesinger wrote:

> Hello,
>
> I am trying to use the PAML result parser (BioPerl
> Bio::Tools::Phylo::PAML) on output files generated by PAML 3.15.
> However on all outputs I have tested no result object is returned
> (next_result is undef). This includes the HIV and Lysin datasets
> included with PAML.
> My code is:
>
> my $codemlp = Bio::Tools::Phylo::PAML->new(-file => "mlc",dir =>
> "/.");
> my $result = $codemlp->next_result;
> foreach my $model ( $result->get_NSSite_results ) {
> ...
>
> and the error is: Can't call method "get_NSSite_results" on an
> undefined value ...
>
> I can include the mlc file is needed. Is this supposed to work? Or do
> I have to run paml from bioperl to parse the results?
>
> Thanks
>   Felix
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> Bioperl-l at lists.open-bio.org
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--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/




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