[Bioperl-l] Bio::TreeIO -> Reconstructing Newick

[Joseph Ryan]

Jason,
Thanks!  That did the trick.
Actually, I didn't specify a -file for $out_treeio and it must have defaulted
to STDOUT.
--Joe

--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> You got to open a new file -
> my $in_treeio = new Bio::TreeIO('-format' => 'newick',
>                                   '-file'   => 'treefile.consense');
> my $out_treeio = new Bio::TreeIO('-format' => 'newick',
>                                   '-file'   => '>NEW_treefile.consense');
> 
> my $tree = $in_treeio->next_tree;
> 
> $out_treeio->write_tree($tree);
> 
> Can't use the same handle for both reading and writing.
> Note the ">" at the front of the filename in the out_treefile
> initialization - this is to tell Perl you are opening a new file.
> 
> You can specify a filehandle like STDOUT or a filehandle you have opened
> somewhere else with the
> -fh => \*STDOUT
> or
> -fh => $otherFH
> 
> in place of the -file  key&value in the init hash.
> 
> HTH,
> Jason
> 
> On Mon, 15 Apr 2002, Joseph Ryan wrote:
> 
> > I am trying to read in a Newick Treefile, make some adjustments to the
> > bootstrap values, and then print back out a treefile.  Reading in the
> treefile
> > is a breeze with the Bio::TreeIO module.
> >
> >     my $treeio = new Bio::TreeIO('-format' => 'newick',
> >                                  '-file'   => 'treefile.consense');
> >
> > Adjusting the bootstrap values should be fairly straight forward, but I
> have
> > come across a snag in trying to generate an updated newick treefile.  I
> tried
> > to use the write_tree method from Bio::TreeIO:
> >
> >     $treeio->write_tree($tree);
> >
> > But I get the following error:
> >
> >     Filehandle Symbol::GEN0 opened only for input at
> > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm
> >
> > Is there an easy way to adjust the output stream?  Maybe to STDOUT?
> >
> > Many thanks,
> > Joe Ryan
> > --


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