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

[Heikki Lehvaslaiho]

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
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     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
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