[Bioperl-l] Saving Codeml Output file
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.
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
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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