[Biopython-dev] [Fwd: Bug in Biopython Phyloxml reader]

[Brad Chapman]

Nicolas;
Thanks for reporting the problem. The Biopython mailing lists
(http://biopython.org/wiki/Mailing_lists) are the right place to
report these types of issues.

Hopefully Eric or someone else on the list will be able to help.
Thanks again,
Brad

----- Forwarded message from Nicolas Rochette <nicolas.rochette at univ-lyon1.fr> -----

Date: Wed, 15 Jun 2011 14:25:09 +0200

Sir,

I apologize for contacting you directly, but I could not find the
right place for this report. Could you please forward it ?

The bug is about 0-length terminal branches being given a length of 1
; please find an example below.

Regards,

Nicolas Rochette
PhD student
Laboratory for Biometry and Evolutive Biology
Lyon, France

//

echo '(A:2,(B:0,C:3):0,D:5);' > foo.newick
java -cp forester.jar org.forester.application.phyloxml_converter
-f=nn -i foo.newick foo.phyloxml
python -c 'from Bio import Phylo;
Phylo.write(Phylo.read("foo.phyloxml","phyloxml"), "bar.newick",
"newick")'
cat bar.newick

(A:2.00000,(B:1.00000,C:3.00000)0.00000:0.00000,D:5.00000)0.00:0.00000;


----- End forwarded message -----