[Biopython] Bug in Phylo.write('phyloxml')?

[Jon Sanders]

Yup, that seems to work just fine, and it's way easier and safer than
writing a script to open the tree file and kill the tag, which is what I
was going to do. Thanks again!

-j

On Mon, Dec 19, 2011 at 12:31 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> Alrighty,
>
> I think the main problem in your case is that the Newick parser creates
> trees with the 'name' attribute set to the empty string "" instead of None.
> When converting to PhyloXML, that value stays in place and gets serialized
> as an empty element. The author of the phyloXML spec is the author of
> Archaeopteryx, so all of that makes sense.
>
> For your case, Jon, and others having this problem: before writing a tree
> as phyloXML, set the tree name to None if it's not already named.
>
> if tree.name == "":
>     tree.name = None
> Phylo.write(tree, 'example.xml', 'newick')
>
>
> For the future, I guess the best approach is to change the Newick parser
> to set the tree name to None instead of "" by default. Any issues with that
> solution?
>
> -Eric
>
>
>
> On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> Archaeopteryx is the one program that read the trees fine. I also tried
>> HyperTree, TreeGraph2, and Treevolution, which failed.
>>
>> -j
>>
>>
>> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>>
>>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>>
>>>> My XML trees exported in biopython (with confidence values, thanks
>>>> Eric!)
>>>> don't open in most XML tree viewing programs.
>>>>
>>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>>> tree.
>>>>
>>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>>  <phy:phylogeny rooted="false">
>>>>    <phy:name />
>>>>    <phy:clade>
>>>>
>>>> If I delete this tag they open fine.
>>>>
>>>>
>>> Hi Jon,
>>>
>>> Thanks for reporting this. I'll check the spec to see if an empty 'name'
>>> tag is even valid. Can you give me the name of one or two programs that are
>>> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
>>> one of them?
>>>
>>> -Eric
>>>
>>
>>
>>
>> --
>> "If you hold a cat by the tail you learn things you cannot learn any
>> other way."
>>                          --Mark Twain
>>
>>
>


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain