[Bioperl-l] PAML Codeml version supported

[Dave Messina]

Hi Laurent,

The last version of PAML/CODEML that I personally verified to work with
BioPerl was 4.3b. Unfortunately, PAML's author has a bad habit of constantly
changing his programs' output format — and constantly releasing new versions
— so it's difficult for us to keep up.

Are you using a relatively recent version of bioperl-live downloaded from
github? If so, would you please file this as a bug? Please include with that
bug a codeml output file from version 4.4 (assuming that's the version you
want to use).

http://bugzilla.open-bio.org/


I haven't tested it, but I think your code is fine — the error you posted is
in the parsing code, not in the run-PAML code.

Incidentally, I'm surprised 3.15 doesn't work because we have tests
specifically for that version that pass AFAIK. But of course tests don't
cover everything.


Dave





On Fri, Feb 18, 2011 at 18:51, Frantz, Laurent <laurent.frantz at wur.nl>wrote:

> Dear Bioperl Gurus,
>
> I have a large set of genes that I need to check separately for dS/dN. I am
> trying to use the Bioperl wrapper for PAML, however I can not get it to
> work.
> I have read that there are problems with the output of newer version of
> PAML that does not fit to the wrapper. I have tried 4.4, 4.1 and then 3.15
> none of those work.
>
> Here is my error message (same with all those versions):
>
> ------------- 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/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::Tools::Phylo::PAML::_parse_summary
> /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:461
> STACK: Bio::Tools::Phylo::PAML::next_result
> /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:270
> STACK: paml_gene_parse.pl:26
> ----------------------------------------------------------------
>
> Could anyone tell me which of the PAML - Codeml versions gives an output
> that can be parsed by Bioperl?
> I am surprised that it does not work with the version 3.15 as it is suppose
> to (http://www.bioperl.org/wiki/PAML).
>
> I am also wondering if my syntax is correct.
>
> @files = @ARGV;
>
> foreach $files (@files) {
>        my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new
>        ( -params => { 'runmode' => -2,
>                        'seqtype' => 1,
>                                   } );
>        $kaks_factory->alignment($files);
>        my ($rc,$parser) = $kaks_factory->run();
>        my $result = $parser->next_result;
>        my $MLmatrix = $result->get_MLmatrix();
>        print "$MLmatrix\n";
> }
>
> The files that I input are already formated for Codeml, they work perfectly
> fine when I feed them myself to Codeml through the config file.
>
> I hope someone can help me..
> Thank you,
>
> Laurent Frantz
> PhD Student - Comparative Genomics
> Wageningen University
> laurent.frantz at wur.nl
>
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