[Bioperl-l] Saving Codeml Output file

Lorenzo Carretero Paulet locarpau at upvnet.upv.es
Mon Aug 29 15:05:49 EDT 2011


Kevin,
Still the same. The previous message is preceeded by:
Filehandle GEN11 opened only for output at /Library/Perl//5.10.0/Bio/Root/IO.pm
line 571
which points to
# if the buffer been filled by _pushback then return the buffer
    # contents, rather than read from the filehandle
    if( @{$self->{'_readbuffer'} || [] } ) {
    $line = shift @{$self->{'_readbuffer'}};
    } else {
    $line = <$fh>;
    }

from the inner subroutine _readline of /Bio/Root/IO.pm
Best,
L

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

> 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?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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