[Bioperl-l] Saving Codeml Output file

Kevin Brown Kevin.M.Brown at asu.edu
Mon Aug 29 14:09:29 EDT 2011


Opening a file for output that does not exist requires the > or >>
redirector (depending on if you want to overwrite or append output).

my $parserF= Bio::Tools::Phylo::PAML->new (-file => ">mlc", -dir =>
"./");



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 Dave Messina
> Sent: Monday, August 29, 2011 10:44 AM
> To: Lorenzo Carretero Paulet
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Saving Codeml Output file
> 
> Hi Lorenzo,
> 
> 
> 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
> >
> 
> 
> > what I guess means the output file is not being saved in the
previous
> step.
> >
> 
> 
> Your interpretation could be correct. I think though that it might be
> that
> the -dir parameter you specify, "./", is not correct. Are you seeing
> the mlc
> file in the '.' (current working) dir?
> 
> If I remember correctly, by default the mlc file is created in a
> temporary
> directory in /scratch or /tmp, and the save_tempfiles flag simply
keeps
> that
> temporary directory from being deleted.
> 
> I don't have the docs in front of me, but I believe there's a way to
> get the
> path of the temp directory that B::T::P::PAML is using. If so, you can
> use
> that path as the value for the -dir parameter.
> 
> Let me know if not, though, and we can follow up on this.
> 
> Dave
> 
> PS - also, could you verify that you're using the latest versions of
> bioperl-live and bioperl-run from Github?
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