TypeError: expect subclass obj of 'AncestralGenome', got ExtantGenome #7
Description
Hi,
I am trying to set up a HAM from the latest OMA release (https://omabrowser.org/oma/current/) as in the tutorial here (https://zoo.cs.ucl.ac.uk/tutorials/tutorial_pyHam_get_started.html).
import pyham
nwk_path = "./speciestree.nwk"
orthoxml_path = "./oma-hogs.orthoXML"
ham_analysis = pyham.Ham(nwk_path, orthoxml_path, use_internal_name=True, tree_format='newick')
It comes back with the following error:
Traceback (most recent call last):
File "<ipython-input-6-9b28b33953bd>", line 1, in <module>
ham_analysis = pyham.Ham(nwk_path, orthoxml_path, use_internal_name=True, tree_format='newick')
File "/Users/ethanbass/Downloads/pyham_master/pyham/ham.py", line 273, in __init__
self.top_level_hogs, self.extant_gene_map, self.external_id_mapper = self._build_hogs_and_genes(orthoxml_file, filter_object=self.filter_obj)
File "/Users/ethanbass/Downloads/pyham_master/pyham/ham.py", line 829, in _build_hogs_and_genes
parser.feed(line)
File "/Users/ethanbass/Downloads/pyham_master/pyham/parsers.py", line 182, in end
hog.set_genome(ancestral_genome)
File "/Users/ethanbass/Downloads/pyham_master/pyham/abstractgene.py", line 245, in set_genome
type(genome).__name__))
TypeError: expect subclass obj of 'AncestralGenome', got ExtantGenome
I would appreciate any insights into what might be causing this problem.
Ethan