[Bioperl-l] Bio::Taxonomy::Tree

[Heikki Lehvaslaiho]

I am glad that you got code working but in general it would be better to
understand where the two enclosed parenthesis pairs arise and fix that.
Maybe Dan Kortschak who wrote the taxonomy modules can help.

	-Heikki

On Sat, 2003-04-05 at 00:05, Qiang TU wrote:
> Hi Heikki,
> 
> Yes, those strange characters may cause trouble. Besides, another problem
> is single branch at several levels may cause many brackets, e.g. (((a,b)),c); 
> and these continuous brackets are illegal for the draw tree softwares. So, I 
> add a condition in the sub _write_tree_Helper in newick.pm to prevent 
> outputting these extra nodes:
> 
> 209,211c209,213
> <       $data[0] = "(" . $data[0];
> <       $data[-1] .= ")";
> <       $data[-1] .= ":". $node->branch_length if( $node->branch_length);
> ---
> >       if (scalar($node->each_Descendent()) > 1) {
> >           $data[0] = "(" . $data[0];
> >           $data[-1] .= ")";
> >           $data[-1] .= ":". $node->branch_length if( $node->branch_length);
> >       }
> 
> 
> Now it works for my problem. But I am not sure if it is a right way to draw 
> trees. Or maybe we can add an option to let user to choice?
> 
> Thanks.
> 
> Qiang Tu
> 
> BTW: I am using bioperl 1.2.
> 
> ---Original Message---
> From: Heikki Lehvaslaiho<heikki at ebi.ac.uk>
> Subject: Re: [Bioperl-l] Bio::Taxonomy::Tree
>  
> >Quing Tu,
> >
> >I found this from
> >http://evolution.genetics.washington.edu/phylip/newicktree.html :
> >
> >"A name can be any string of printable characters except blanks,
> > colons, semicolons, parentheses, and square brackets.
> >
> > Because you may want to include a blank in a name, it is assumed that
> > an underscore character ("_") stands for a blank; any of these in a
> > name will be converted to a blank when it is read in."
> >
> >
> >I am adding the conversion into Bio::Tree::Node::id.
> >The method will print a warning, too, if $node->verbose >=0
> >
> >Check the CVS after a while.
> >
> >	-Heikki
> >
> >On Thu, 2003-04-03 at 17:02, Heikki Lehvaslaiho wrote:
> >> Your tree looks OK. I did not try to it with any program, so this is
> >> just a wild guess, but try removing spaces from the tree and try again.
> >> 
> >> 	-Heikki
> >> 
> >> 
> >> 
> >> On Thu, 2003-04-03 at 14:02, Qiang Tu wrote:
> >> > Hello all,
> >> > 
> >> > I want to build a taxonomy tree of the complete genomes. In the program I 
> >> > built a Bio::Taxonomy::Taxon object at first, then use 'set_root_node' method
> >> > to built a Bio::Taxonomy::Tree objxect by the taxon, then write the tree to a file 
> >> > by Bio::TreeIO object. The 'tabtree' method works, but the output files of 
> >> > 'newick' and 'nhx' methods can not be opened by other draw-tree software, 
> >> > such as treeview. The error message is: Extra pair of parentheses "()".
> >> > The tree file is attached.
> >> > 
> >> > Has anyone ever made such a taxonomy tree? Could you give me some samples
> >> > so that I can find out the solution of my problem? Thanks. 
> >> >  
> >> > Qiang Tu
> >> > Institute of Biochemistry and Cell Biology
> >> > Chinese Academy of Sciences
> >> > 
> >> > ______________________________________________________________________
> >> > 
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > Bioperl-l at bioperl.org
> >> > http://bioperl.org/mailman/listinfo/bioperl-l
> >-- 
> >______ _/      _/_____________________________________________________
> >      _/      _/                      http://www.ebi.ac.uk/mutations/
> >     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
> >    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> >___ _/_/_/_/_/________________________________________________________
> >
> >
> 
>  
> ---End of Message---
> 
>  
> Qiang Tu
> Institute of Biochemistry and Cell Biology
> Chinese Academy of Sciences
> Email: tuqiang at mail.shcnc.ac.cn, tuqiang_cn at yahoo.com
>   
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________