[Bioperl-l] Saving Codeml Output file

Kevin Brown Kevin.M.Brown at asu.edu
Mon Aug 29 15:19:53 EDT 2011


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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