ete
ete copied to clipboard
etetoolkit
Props debugging phylo
one branch that comnied debugged result of clustering phylo and ncbi_taxanomy
unitest command:
python -m "ete4.test.test_phylotree
python -m "ete4.test.test_arraytable
python -m "ete4.test.test_clustertree
python -m "ete4.test.test_ncbiquery
It was designed to seperate but phylo and ncbiquery were actually easier debug together, so..... If you have any question, let me know
To be continued.... "Props debugging gtdb" and "Props debugging ete_diff"
python -m "ete4.test.test_phylotree
FAILED: wrong writing of tree without explicit distance. Default distance is now -1 => error when comparing trees (old default I believe was one.... weird if the root gets this value by default and not the rest of the tree..). @jhcepas, should we change the default branch length value to something different to "-1" in the new ETE parser ?
python -m "ete4.test.test_arraytable
Succeded. Just changed deprecated method "assert_" to "assertTrue" im test_arraytable.py
python -m "ete4.test.test_clustertree
SUCCEDED. Needs scipy module to run test