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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
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Props debugging phylo #570

Closed dengzq1234 closed 1 year ago

dengzq1234 commented 3 years ago

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"

jorgebotas commented 3 years ago

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 ?

jorgebotas commented 3 years ago

python -m "ete4.test.test_arraytable

Succeded. Just changed deprecated method "assert_" to "assertTrue" im test_arraytable.py

jorgebotas commented 3 years ago

python -m "ete4.test.test_clustertree

SUCCEDED. Needs scipy module to run test

jorgebotas commented 3 years ago

python -m "ete4.test.test_ncbiquery

SUCCEDED. Only NCBI warnings

jorgebotas commented 3 years ago

Changes should be merged. Pending tree writing default dist "bug"