[Bioperl-l] Saving Codeml Output file

Lorenzo Carretero Paulet locarpau at upvnet.upv.es
Mon Aug 29 19:19:46 EDT 2011


Kevin,
That's pretty reasonable, but unfortunately still doesn't run. Even if I create
the file as $outfile and give it as value to the wrapper as -outfile
=>$outfile. It seems as if Bio::Tools::Run::Phylo::PAML::Codeml failed at
creating the outfile. Did anyone manage to generate the outfile from
Bio::Tools::Run::Phylo::PAML::Codeml.
Cheers,
Lorenzo

 Mensaje citado por Kevin Brown <Kevin.M.Brown at asu.edu>:

> OK, went back to the original message.
>
> And here's where the problem actually originates...
>
> my $codeml_factory = new Bio::Tools::Run::Phylo::PAML::Codeml
>  						(
> 				# this should cause it to create a file
> called mlc
> 						-outfile => '>mlc',
> 						-save_tempfiles => 1,
>  						-alignment =>
> $codon_MSA,
>  						-tree =>
> $biotree,
>  						-params =>
>  {
>   	'verbose' => 1,
>  	'noisy' => 9,
>  	'runmode' => 0, #user tree
>  	'seqtype' => 1,
>  	'model' => $model,
>  	'NSsites' => $NSsites,
>  	'fix_omega' => $fix_omega,
>  	'omega' => $omega,
>  	'ncatG' => $ncatG,
>  	'icode' => 0, #* 0:universal code; 1:mammalian mt; 2-10:see
> below (5:ciliate nuclear)
>  	#'fix_alpha' => 0,
>  	#'fix_kappa' => 0,
> 	#'RateAncestor' => 0,
> 	'CodonFreq' => 2,
> 	'cleandata' => 1, # remove sites with amibguity data (1 yes, 0
> no),
> 	'ndata' => 1
>  },
> );
>
>
> Kevin Brown
> Center for Innovations in Medicine
> Biodesign Institute
> Arizona State University
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Lorenzo Carretero Paulet
> > Sent: Monday, August 29, 2011 9:47 AM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Saving Codeml Output file
> >
> > Hi all,
> > I'm running codeml from the PAML package using the corresponding
> > Bioperl
> > wrapper. I'd like to save the output file as -outfile => 'mlc', as in:
> > my $codeml_factory = new Bio::Tools::Run::Phylo::PAML::Codeml
> > 						( -outfile => 'mlc',
> > 						-save_tempfiles => 1,
> > 						-alignment =>
> $codon_MSA,
> > 						-tree =>
> $biotree,
> > 						-params =>
> > {
> > #'outfile' =>'mlc',
> > 	'verbose' => 1,
> > 	'noisy' => 9,
> > 'runmode' => 0, #user tree
> > 'seqtype' => 1,
> > 'model' => $model,
> > 'NSsites' => $NSsites,
> > 'fix_omega' => $fix_omega,
> > 'omega' => $omega,
> > 'ncatG' => $ncatG,
> > 'icode' => 0, #* 0:universal code; 1:mammalian mt; 2-10:see below
> > (5:ciliate
> > nuclear)
> > 	#'fix_alpha' => 0,
> > 	#'fix_kappa' =>
> > 0,							#'RateAncestor'
> => 0,
> > 							'CodonFreq' =>
> 2,
> > 						'cleandata' =>
> > 1, # remove sites with amibguity data (1 yes, 0 no),
> > 'ndata' => 1
> >
> },
> > 						);
> >
> > and subsequently parsing it using
> > my $parserF= Bio::Tools::Phylo::PAML->new (-file => "mlc", -dir =>
> > "./");
> >
> > However, I get the following message.
> >
> > ------------- EXCEPTION -------------
> > MSG: Could not open mlc: No such file or directory
> > STACK Bio::Root::IO::_initialize_io
> > /Library/Perl//5.10.0/Bio/Root/IO.pm:351
> > STACK Bio::Tools::Phylo::PAML::new
> > /Library/Perl//5.10.0/Bio/Tools/Phylo/PAML.pm:239
> > STACK main::BranchSiteEvolAnalysis
> > /Users/marioafares/Documents/workspace/BactEvolGen/BactEvolGen.pl:1421
> > STACK toplevel
> > /Users/marioafares/Documents/workspace/BactEvolGen/BactEvolGen.pl:939
> > -------------------------------------
> >
> > what I guess means the output file is not being saved in the previous
> > step.
> > Anyone knows what's wrong.
> > Tnak you very much in advance for your help.
> > Cheers,
> > Lorenzo
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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