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

[Eric Talevich]

Hi Nicolas and Brad,

Thanks for reporting and forwarding this. The 0 -> 1 terminal branch lengths
are another surprising default that crept in during the port of NewickIO; I
don't see a problem with changing it to keep 0-length branches at the tips.
The phyloXML parser and writer shouldn't be introducing this bug; it should
just be occurring when writing in Newick or Nexus formats.

I'll keep you posted on the fix, probably this weekend. If you'd like to try
it yourself, the code to edit is in Bio/Phylo/NewickIO.py.

Best,
Eric

On Wed, Jun 15, 2011 at 9:03 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

> 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 -----
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