[Bioperl-l] TreeIO problem

[Mikel Egaa9pen-b]

Yes, that's right;

I forgot to install SVG::Graph, I have installed it and the script
works... but the output file is void!

the -w option doesn't give any clues. 

I have been having a brief look into SVG::Graph and
Bio::TreeIO::svggraph and I cannot figure out what should be wrong.

Regards.  

On Thu, 15 Apr 2004 12:44:14 -0400 (EDT)
Jason Stajich <jason at cgt.duhs.duke.edu> wrote:

> And you did install SVG::Graph... which pulls in a bunch of
> dependancies:
> 
>  Math::Derivative
>  Math::Spline
>  Tree::DAG_Node
> 
> 
> What does 'perldoc SVG::Graph' report?
> 
> If I do the install via the cpan shell I get all the dependancies too.
> -jason
> 
> On Thu, 15 Apr 2004, Mikel [ISO-8859-1] Ega wrote:
> 
> > Hello people;
> >
> > First of all, Bioperl is great. I have just started using it for one
> > of my projects and I'm amazed.
> >
> > I have a problem with the TreeIO class. I just want to write a
> > newick tree in SVG format, so I got this code from the api and put
> > it in this little script:
> >
> > -------------------------------------------------------------------
> > -----#!/usr/bin/perl
> >
> > use Bio::TreeIO;
> >
> > my $in = new Bio::TreeIO(-file => 'input', -format => 'newick');
> > my $out = new Bio::TreeIO(-file => '>output', -format =>
> > 'svggraph');
> >
> >   while( my $tree = $in->next_tree ) {
> >       my $svg_xml = $out->write_tree($tree);
> >   }
> >
> > -------------------------------------------------------------------
> > -----
> >
> > And the following exception was given:
> >
> > -------------------------------------------------------------------
> > ----- MSG: Failed to load module Bio::TreeIO::svggraph. Can't locate
> > SVG/Graph.pm in @INC (@INC contains: /etc/perl
> > /usr/local/lib/perl/5.8.3/usr/local/share/perl/5.8.3 /usr/lib/perl5
> > /usr/share/perl5/usr/lib/perl/5.8 /usr/share/perl/5.8
> > /usr/local/lib/site_perl .)
> > at/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. BEGIN
> > failed--compilation aborted
> > at/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78.
> > Compilation failed in require at
> > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm line 394.
> >
> > STACK Bio::Root::Root::_load_module
> > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm:396 STACK (eval)
> > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:227 STACK
> > Bio::TreeIO::_load_format_module
> > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:226 STACK Bio::TreeIO::new
> > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:126 STACK toplevel
> > ./svg.pl:6---------------------------------------------------------
> > ---------------
> >
> > So I have installed all the SVG related modules via CPAN but I
> > receive the same error, and I cannot figure out what should I do
> > next.
> >
> > Thank you for your time,
> >
> > Mikel Egaña.
> >
> > PS: I'm using bioperl 1.4 in Debian Sarge.
> >
> > -------------------------------------------------
> > -->pik at lolita (Debian Sarge-Kernel 2.4.20)
> >
> > -->http://sindominio.net/~pik
> >
> > -->"Don Quijote se salva cuando se echa a
> >    los caminos a ser apaleado" (Francisco Umbral)
> > -------------------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l


-------------------------------------------------
-->pik at lolita (Debian Sarge-Kernel 2.4.20) 

-->http://sindominio.net/~pik

-->"Don Quijote se salva cuando se echa a 
   los caminos a ser apaleado" (Francisco Umbral)
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