[Bioperl-l] parsing paml output

Jason Stajich jason at bioperl.org
Fri May 8 12:57:54 EDT 2009

The parsing is decoupled that is Bio::Tools::Phylo::PAML and I'm  
pretty sure where the errors are coming from.

I think a sample report and sample script as a bug report is a good  
first step in case this a simple problem to diagnose.

However we need programmers who want to work on this problem to step  
up and help update the module to deal with new variants in the PAML  
output file format.
I think we've failed to recruit any new developers to work on  
supporting the latest PAML so things work(ed) for 3.15 but I think 4  
has new variations in the format that cause it to fall over.

On May 8, 2009, at 9:43 AM, Albert Vilella wrote:

> 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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Jason Stajich
jason at bioperl.org

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