[Bioperl-l] parsing paml output

Albert Vilella avilella at gmail.com
Fri May 8 12:43:55 EDT 2009

If I remember correctly, there was a way to just parse the output that is
decoupled of running PAML through bioperl.
I am ccing the bioperl mailing list as I've seen people having parsing
issues with some newer versions of PAML.

What version are you trying to parse? Can you attach a small example?

On Fri, May 8, 2009 at 4:44 PM, Irene Newton <irene.newton at gmail.com> wrote:

> Hello!
> I first want to thank you for contributing your module to the bioperl
> community.  Every time I think, "hey, wouldn't it be great if someone coded
> this tool?" It's there!  It's much appreciated.
> I've been trying to implement it but am confused about one thing: what is
> the main codeml output file that the parser expects?  I usually work with
> the *.out files or the rst files but when I try either of those as input,
> the parser throws an error:
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Unknown format of PAML output
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.8.8/Bio/Root/Root.pm:328
> STACK: Bio::Tools::Phylo::PAML::_parse_summary
> /usr/local/share/perl/5.8.8/Bio/Tools/Phylo/PAML.pm:359
> STACK: Bio::Tools::Phylo::PAML::next_result
> /usr/local/share/perl/5.8.8/Bio/Tools/Phylo/PAML.pm:224
> STACK: ./paml_parser.pl:14
> ----------------------------------------------------------------
> Any thoughts?  Warm regards,
> Irene
> --
> Irene L.G. Newton
> Postdoctoral Fellow
> Tufts University - Microbiology Department
> Jaharis 424
> 136 Harrison Ave.
> Boston, MA 02111

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