[Bioperl-l] Error calling alignment method

[Lorenzo Carretero Paulet]

El 25/05/11 20:44, Dave Messina escribió:
> Hi Lorenzo,
>
> You've got a typo in your variable names.
>
>     my $ks_factory
>
>
>     my $kaks_factory->alignment($dna_aln);
>
>
> So I think it's the $kaks_factory that's undefined. And furthermore, 
> no my in front of the method call.
>
> I'm not sure how this even compiles — I guess the check for method 
> calls happens at runtime, so that's why the stray "my" is missed.
>
>
> Also, a request: I really appreciate you posting your code and 
> including your data files. However, email tends to wrap lines funny, 
> which breaks code. In the future could you try attaching your code 
> also, or using gists (https://gist.github.com/) ?
>
> Thanks,
> Dave
>
>
Thanks Dave.
I attach a corrected version of the code and both nt and aa files. It's 
still not working, returning the message:

------------- EXCEPTION Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK Bio::Tools::Phylo::PAML::_parse_summary 
/Library/Perl//5.10.0/Bio/Tools/Phylo/PAML.pm:461
STACK Bio::Tools::Phylo::PAML::next_result 
/Library/Perl//5.10.0/Bio/Tools/Phylo/PAML.pm:270
STACK main::GettingBioperlAlignmentAAtoDNAplusPAMLcalculation 
/Users/marioafares/Documents/workspace/PlantEvolGen/test.pl:154
STACK toplevel 
/Users/marioafares/Documents/workspace/PlantEvolGen/test.pl:35
---------------------------------------------------------------

I think the codon alignment is being proberly constructed by the method 
aa_to_dna_aln, as I can do a Dumper printing of it. So the problem must 
be in the PAML codeml wrapper not properly recognizing the codon 
alignment. Could it be related to the alignment format (PAML runs on 
PHYLIP formatted files)?
Cheers,
Lorenzo



-- 
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Lorenzo Carretero Paulet
Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
Integrative Systems Biology Group
C/ Ingeniero Fausto Elio s/n.
46022 Valencia, Spain

Phone:  +34 963879934
Fax:    +34 963877859
e-mail: locarpau at upvnet.upv.es
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