internal node naming bug
max-baer opened this issue · 1 comments
When running the following code, the internal node naming yields the number 1 as name:
Python 3.9.5 (default, Nov 4 2021, 14:38:27)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
import pyham
import logging
logging.basicConfig(level=logging.INFO, format="%(asctime)s %(name)-12s %(levelname)-8s %(message)s")
orthoxml_path = "./Output/HierarchicalGroups.orthoxml"
nwk_path = "./Output/EstimatedSpeciesTree.nwk"
tree_str = pyham.utils.get_newick_string(nwk_path, type="nwk")
ham_analysis = pyham.Ham(tree_str, orthoxml_path, use_internal_name=True)
2023-12-04 14:01:34,749 pyham.ham INFO Build taxonomy: completed.
2023-12-04 14:01:34,985 pyham.parsers INFO Species trichinella created.
2023-12-04 14:01:35,099 pyham.parsers INFO Species trichuris_1 created.
2023-12-04 14:01:35,343 pyham.parsers INFO Species trichuris_2 created.
2023-12-04 14:01:35,473 pyham.parsers INFO Species trichuris_3 created.
2023-12-04 14:01:35,571 pyham.parsers INFO Species trichuris_4 created.
2023-12-04 14:01:35,728 pyham.parsers INFO Species trichuris_5 created.
2023-12-04 14:01:35,825 pyham.parsers INFO Species trichuris_6 created.
2023-12-04 14:01:35,991 pyham.parsers INFO Species trichuris_7 created.
2023-12-04 14:01:36,014 pyham.parsers INFO 500 HOGs parsed.
2023-12-04 14:01:36,038 pyham.parsers INFO 1000 HOGs parsed.
2023-12-04 14:01:36,060 pyham.parsers INFO 1500 HOGs parsed.
2023-12-04 14:01:36,083 pyham.parsers INFO 2000 HOGs parsed.
2023-12-04 14:01:36,112 pyham.parsers INFO 2500 HOGs parsed.
2023-12-04 14:01:36,152 pyham.parsers INFO 3000 HOGs parsed.
2023-12-04 14:01:36,190 pyham.parsers INFO 3500 HOGs parsed.
2023-12-04 14:01:36,242 pyham.parsers INFO 4000 HOGs parsed.
2023-12-04 14:01:36,308 pyham.parsers INFO 4500 HOGs parsed.
2023-12-04 14:01:36,421 pyham.parsers INFO 5000 HOGs parsed.
2023-12-04 14:01:36,523 pyham.parsers INFO 5500 HOGs parsed.
2023-12-04 14:01:36,615 pyham.parsers INFO 6000 HOGs parsed.
2023-12-04 14:01:36,846 pyham.parsers INFO 6500 HOGs parsed.
2023-12-04 14:01:37,094 pyham.parsers INFO 7000 HOGs parsed.
2023-12-04 14:01:37,215 pyham.parsers INFO 7500 HOGs parsed.
2023-12-04 14:01:37,329 pyham.parsers INFO 8000 HOGs parsed.
2023-12-04 14:01:37,449 pyham.parsers INFO 8500 HOGs parsed.
2023-12-04 14:01:37,568 pyham.parsers INFO 9000 HOGs parsed.
2023-12-04 14:01:37,685 pyham.parsers INFO 9500 HOGs parsed.
2023-12-04 14:01:37,805 pyham.parsers INFO 10000 HOGs parsed.
2023-12-04 14:01:37,891 pyham.parsers INFO 10500 HOGs parsed.
2023-12-04 14:01:37,977 pyham.parsers INFO 11000 HOGs parsed.
2023-12-04 14:01:38,125 pyham.parsers INFO 11500 HOGs parsed.
2023-12-04 14:01:38,397 pyham.parsers INFO 12000 HOGs parsed.
2023-12-04 14:01:38,533 pyham.parsers INFO 12500 HOGs parsed.
2023-12-04 14:01:38,676 pyham.parsers INFO 13000 HOGs parsed.
2023-12-04 14:01:38,811 pyham.parsers INFO 13500 HOGs parsed.
2023-12-04 14:01:38,936 pyham.parsers INFO 14000 HOGs parsed.
2023-12-04 14:01:38,954 pyham.ham INFO Parse Orthoxml: 14126 top level hogs and 113889 extant gene s extract.
2023-12-04 14:01:38,954 pyham.ham INFO Set up Ham analysis: ready to go with 14126 hogs founded wi thin 8 species.
for ag in ham_analysis.taxonomy.internal_nodes:
... print("\t- {}".format(ag.name))
...
- 1
- 1
- 1
-
- 0.33416289
- 1
- 1
Worked by setting use_internal_name=False