Closed gmartinezredondo closed 2 years ago
Hi @gmartinezredondo
The problem with your test orthoxml is that the orthoxml namespace is not defined. you need to include in <orthoXML>
tag the xmlns
attribute with http://orthoXML.org/2011/
. Then it seems to work:
<orthoXML xmlns="http://orthoXML.org/2011/">
<species name="Dme">
...
</orthoXML>
That works!
Thank you very much, Adrian!
Hi!
I am trying to use the TreeProfile tool in pyHam to visualize gene evolution. I am first testing the tool with a dummy dataset and obtained my orthoXML file using ETE3. However, when I try to execute the functions from the tutorial, an error raises. I have explored a little bit and it seems that the output of
pyham.Ham(tree_str, orthoxml_path, use_internal_name=False)
is empty, while it is not when I use the example orthoXML. For example, the list of extant genes I get is empty, but it should not be.I attach the orthoXML file I am using.
Does the orthoXML file have to have additional information that I am not including?
This is the code I have used, in case I did something wrong:
And the error it raises (which I think is caused by the empty Ham object):