[Bioperl-l] Saving Codeml Output file

Janet Young jayoung at fhcrc.org
Tue Mar 6 13:55:26 EST 2012

Lorenzo Carretero Paulet <locarpau <at> upvnet.upv.es> writes:

> Thanks Jason,
> Ok, I see. That's what I was triying at the beggining. This runs OK in my
> scripts  for
> branch-specific models. However, when I try branch-site models (NSsites > 0)
> and try to parse the results using
> my $model_result= $paml_result->get_NSSite_results
> I start to have problems.
> That's why I was trying to save the mlc output file and parse it, instead of
> parsing directly the Bio::Tools::Phylo::PAML object.

Hi Lorenzo,

I just ran into a similar issue (trying to save the output files 
for debugging purposes) and found your email thread.  I managed 
to retrieve the output files by adding this code (after the 
"$codeml_factory->run" step).

my $tempdir = $codeml_factory->tempdir;
system("cp $tempdir/* .");

Maybe that'll help me debug some issues I'm having with parsing a minority of 
my paml runs - we'll see. It might be beyond my skills.


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