[Bioperl-l] met a problem when run Bio::Tools::Run::Phylo::PAML::Yn00

[Chris Fields]

kevin,

As Dave mentioned, go ahead and attach any output from PAML 4.2 to the  
bug report.  I want to make it a priority to get the PAMLM parser  
working for the 1.6 release series (if not 1.6.1, maybe 1.6.2).

chris

On Feb 9, 2009, at 7:39 AM, kevin fan wrote:

>
> hi, chris
> thank you for the reply. i will use PAML 3.15 instead
>
> cheers,
> kevin
> 2009/2/9 Chris Fields <cjfields at illinois.edu>
> We do not adequately support PAML v4.0 and up at this time.  Much of  
> this is due to PAML's constantly shifting output (every release  
> seems to break our parsers).
>
> chris
>
>
> On Feb 9, 2009, at 5:57 AM, kevin fan wrote:
>
> Dear all,
> i am using Bio::Tools::Run::Phylo::PAML::Yn00  to calculate Ka/Ks  
> ratio of
> pairwise sequences.
> bioperl version is 1.6, and PAML version is 4.2
>
> when i run the Bio::Tools::Run::Phylo::PAML::Yn00 , it warns:
>
> -------------------- WARNING ---------------------
> MSG: There was an error - see error_string for the program output
> ---------------------------------------------------
>
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Unknown format of PAML output did not see seqtype
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:359
> STACK: Bio::Tools::Phylo::PAML::_parse_summary
> /usr/local/share/perl/5.10.0/Bio/Tools/Phylo/PAML.pm:441
> STACK: Bio::Tools::Phylo::PAML::next_result
> /usr/local/share/perl/5.10.0/Bio/Tools/Phylo/PAML.pm:257
> STACK: kaks.pl:10
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