[Bioperl-l] Saving Codeml Output file

Lorenzo Carretero Paulet locarpau at upvnet.upv.es
Mon Aug 29 14:56:50 EDT 2011


Thanks Dave,
Yes. I do not found the output file in the current directory, or in the temp
directory. Using
my $tmpdir = $codeml_factory->tempdir();
my $parserF= Bio::Tools::Phylo::PAML->new (										-file => "mlc",
-dir => "$tmpdir"									);
I still get the same error message.
I'm using Bioperl version 1.006901.
Cheers,
Lorenzo

Mensaje citado por Dave Messina <David.Messina at sbc.su.se>:

> 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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