[Bioperl-l] PAML parser

Felix Schlesinger schlesi at ebi.ac.uk
Tue Jun 26 10:59:13 EDT 2007


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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